Getting Started

¶ Author: Brian M. Schilder

¶ Updated: Oct-30-2022

Source: vignettes/echoannot.Rmd 
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##   +.gg   ggplot2

Import data

To get the full dataset of all fine-mapped Parkinson’s Disease loci, you can use the following function:

merged_DT <- echodata::get_Nalls2019_merged()

Annotate

Annotate SNP-wise fine-mapping results.

Here, we’re only annotating a small number of SNPs high-confidence causal SNPs for demo purposes. The more SNPs you supply to annotate_snps, the longer it will take to query the selected databases for each SNP.

#### Only query high-confidence fine-mapping SNPs from one locus ####
dat <- merged_DT[Locus=="LRRK2" & Consensus_SNP==TRUE,]
#### Query annotations ####
dat_annot <- echoannot::annotate_snps(dat = dat,
                                      haploreg_annotation = TRUE, 
                                      regulomeDB_annotation = TRUE,
                                      biomart_annotation = TRUE) 
## Loading required namespace: haploR
## + Gathering annotation data from HaploReg...
## ++ Submitting chunk 1 / 1
## + Gathering annotation data from HaploReg...
## ++ Submitting chunk 1 / 1
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## + Gathering annotation data from Biomart...
knitr::kable(dat_annot)
SNP Locus CHR POS P Effect StdErr Freq MAF N_cases N_controls proportion_cases A1 A2 leadSNP ABF.CS ABF.PP SUSIE.CS SUSIE.PP POLYFUN_SUSIE.CS POLYFUN_SUSIE.PP FINEMAP.CS FINEMAP.PP Mb Support Consensus_SNP mean.PP mean.CS N t_stat chr pos_hg38 r2 D’ is_query_snp ref alt AFR AMR ASN EUR GERP_cons SiPhy_cons Chromatin_States Chromatin_States_Imputed Chromatin_Marks DNAse Proteins eQTL gwas grasp Motifs GENCODE_id GENCODE_name GENCODE_direction GENCODE_distance RefSeq_id RefSeq_name RefSeq_direction RefSeq_distance dbSNP_functional_annotation query_snp_rsid Promoter_histone_marks Enhancer_histone_marks regulome.start regulome.end features.ChIP features.DNase features.Footprint features.Footprint_matched features.IC_matched_max features.IC_max features.PWM features.PWM_matched features.QTL regulome_score.probability regulome_score.ranking allele chr_name chrom_start chrom_end chrom_strand ensembl_gene_stable_id consequence_type_tv polyphen_prediction polyphen_score sift_prediction sift_score reg_consequence_types validated
rs11175620 LRRK2 12 40610864 0 0.1307 0.0142 0.1200 0.1200 56306 1417791 0.0382 C G FALSE NA NA 3 1 3 1 NA NA 40.61086 2 TRUE 0.50 0 216621 9.204225 12 40217062 0 0 0 G C 0.11 0.06 0.00 0.11 0 0 E023,7_Enh;E024,7_Enh;E028,7_Enh;E029,7_Enh;E030,2_TssAFlnk;E031,2_TssAFlnk;E032,7_Enh;E035,1_TssA;E052,7_Enh;E080,7_Enh;E114,7_Enh;E117,7_Enh;E119,7_Enh;E124,2_TssAFlnk E023,16_EnhW1;E025,19_DNase;E028,19_DNase;E029,14_EnhA2;E030,13_EnhA1;E031,14_EnhA2;E032,22_PromP;E033,16_EnhW1;E035,16_EnhW1;E036,14_EnhA2;E037,22_PromP;E038,22_PromP;E039,22_PromP;E040,22_PromP;E041,22_PromP;E042,22_PromP;E043,22_PromP;E044,22_PromP;E045,22_PromP;E046,22_PromP;E048,22_PromP;E050,22_PromP;E051,16_EnhW1;E057,22_PromP;E062,16_EnhW1;E071,22_PromP;E080,22_PromP;E086,19_DNase;E088,22_PromP;E112,17_EnhW2;E113,16_EnhW1;E114,19_DNase;E117,19_DNase;E124,13_EnhA1 E011,H3K4me1_Enh;E018,H3K4me1_Enh;E023,H3K4me1_Enh;E024,H3K4me1_Enh;E025,H3K4me1_Enh;E028,H3K4me1_Enh;E029,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E032,H3K4me1_Enh;E036,H3K4me1_Enh;E049,H3K4me1_Enh;E050,H3K4me1_Enh;E052,H3K4me1_Enh;E056,H3K4me1_Enh;E057,H3K4me1_Enh;E080,H3K4me1_Enh;E086,H3K4me1_Enh;E088,H3K4me1_Enh;E113,H3K4me1_Enh;E114,H3K4me1_Enh;E117,H3K4me1_Enh;E119,H3K4me1_Enh;E124,H3K4me1_Enh;E023,H3K4me3_Pro;E030,H3K4me3_Pro;E031,H3K4me3_Pro;E035,H3K4me3_Pro;E109,H3K4me3_Pro;E124,H3K4me3_Pro;E025,H3K9ac_Pro;E029,H3K27ac_Enh;E032,H3K27ac_Enh;E080,H3K27ac_Enh;E113,H3K27ac_Enh;E124,H3K27ac_Enh E006;E021;E029;E046;E080;E086;E088;E117;E120;E124 . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,3.29211855956645e-07;GTEx2015_v6,Artery_Tibial,LRRK2,1.08781866153343e-11;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,1.72128347769633e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,5.31856078341246e-10;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,1.00796507632068e-05;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.06318553434241e-05;Westra2013,Whole_Blood,-,1.3808392059010189E-31;Westra2013,Whole_Blood,LRRK2,2.116806823753094E-5 . . BCL_disc5;HDAC2_disc3 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 7947 . rs11175620 BLD FAT, ESC, BRST, BLD, MUS, ADRL, LNG, CRVX 40610863 40610864 TRUE TRUE FALSE FALSE 0 0 FALSE FALSE FALSE 0.60906 4 G/C 12 40610864 40610864 1 ENSG00000225342 non_coding_transcript_variant NA NA NA NA 1000Genomes,Frequency,gnomAD,TOPMed
rs11175620 LRRK2 12 40610864 0 0.1307 0.0142 0.1200 0.1200 56306 1417791 0.0382 C G FALSE NA NA 3 1 3 1 NA NA 40.61086 2 TRUE 0.50 0 216621 9.204225 12 40217062 0 0 0 G C 0.11 0.06 0.00 0.11 0 0 E023,7_Enh;E024,7_Enh;E028,7_Enh;E029,7_Enh;E030,2_TssAFlnk;E031,2_TssAFlnk;E032,7_Enh;E035,1_TssA;E052,7_Enh;E080,7_Enh;E114,7_Enh;E117,7_Enh;E119,7_Enh;E124,2_TssAFlnk E023,16_EnhW1;E025,19_DNase;E028,19_DNase;E029,14_EnhA2;E030,13_EnhA1;E031,14_EnhA2;E032,22_PromP;E033,16_EnhW1;E035,16_EnhW1;E036,14_EnhA2;E037,22_PromP;E038,22_PromP;E039,22_PromP;E040,22_PromP;E041,22_PromP;E042,22_PromP;E043,22_PromP;E044,22_PromP;E045,22_PromP;E046,22_PromP;E048,22_PromP;E050,22_PromP;E051,16_EnhW1;E057,22_PromP;E062,16_EnhW1;E071,22_PromP;E080,22_PromP;E086,19_DNase;E088,22_PromP;E112,17_EnhW2;E113,16_EnhW1;E114,19_DNase;E117,19_DNase;E124,13_EnhA1 E011,H3K4me1_Enh;E018,H3K4me1_Enh;E023,H3K4me1_Enh;E024,H3K4me1_Enh;E025,H3K4me1_Enh;E028,H3K4me1_Enh;E029,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E032,H3K4me1_Enh;E036,H3K4me1_Enh;E049,H3K4me1_Enh;E050,H3K4me1_Enh;E052,H3K4me1_Enh;E056,H3K4me1_Enh;E057,H3K4me1_Enh;E080,H3K4me1_Enh;E086,H3K4me1_Enh;E088,H3K4me1_Enh;E113,H3K4me1_Enh;E114,H3K4me1_Enh;E117,H3K4me1_Enh;E119,H3K4me1_Enh;E124,H3K4me1_Enh;E023,H3K4me3_Pro;E030,H3K4me3_Pro;E031,H3K4me3_Pro;E035,H3K4me3_Pro;E109,H3K4me3_Pro;E124,H3K4me3_Pro;E025,H3K9ac_Pro;E029,H3K27ac_Enh;E032,H3K27ac_Enh;E080,H3K27ac_Enh;E113,H3K27ac_Enh;E124,H3K27ac_Enh E006;E021;E029;E046;E080;E086;E088;E117;E120;E124 . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,3.29211855956645e-07;GTEx2015_v6,Artery_Tibial,LRRK2,1.08781866153343e-11;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,1.72128347769633e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,5.31856078341246e-10;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,1.00796507632068e-05;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.06318553434241e-05;Westra2013,Whole_Blood,-,1.3808392059010189E-31;Westra2013,Whole_Blood,LRRK2,2.116806823753094E-5 . . BCL_disc5;HDAC2_disc3 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 7947 . rs11175620 BLD FAT, ESC, BRST, BLD, MUS, ADRL, LNG, CRVX 40610863 40610864 TRUE TRUE FALSE FALSE 0 0 FALSE FALSE FALSE 0.60906 4 G/C 12 40610864 40610864 1 ENSG00000225342 intron_variant NA NA NA NA 1000Genomes,Frequency,gnomAD,TOPMed
rs11175620 LRRK2 12 40610864 0 0.1307 0.0142 0.1200 0.1200 56306 1417791 0.0382 C G FALSE NA NA 3 1 3 1 NA NA 40.61086 2 TRUE 0.50 0 216621 9.204225 12 40217062 0 0 0 G C 0.11 0.06 0.00 0.11 0 0 E023,7_Enh;E024,7_Enh;E028,7_Enh;E029,7_Enh;E030,2_TssAFlnk;E031,2_TssAFlnk;E032,7_Enh;E035,1_TssA;E052,7_Enh;E080,7_Enh;E114,7_Enh;E117,7_Enh;E119,7_Enh;E124,2_TssAFlnk E023,16_EnhW1;E025,19_DNase;E028,19_DNase;E029,14_EnhA2;E030,13_EnhA1;E031,14_EnhA2;E032,22_PromP;E033,16_EnhW1;E035,16_EnhW1;E036,14_EnhA2;E037,22_PromP;E038,22_PromP;E039,22_PromP;E040,22_PromP;E041,22_PromP;E042,22_PromP;E043,22_PromP;E044,22_PromP;E045,22_PromP;E046,22_PromP;E048,22_PromP;E050,22_PromP;E051,16_EnhW1;E057,22_PromP;E062,16_EnhW1;E071,22_PromP;E080,22_PromP;E086,19_DNase;E088,22_PromP;E112,17_EnhW2;E113,16_EnhW1;E114,19_DNase;E117,19_DNase;E124,13_EnhA1 E011,H3K4me1_Enh;E018,H3K4me1_Enh;E023,H3K4me1_Enh;E024,H3K4me1_Enh;E025,H3K4me1_Enh;E028,H3K4me1_Enh;E029,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E032,H3K4me1_Enh;E036,H3K4me1_Enh;E049,H3K4me1_Enh;E050,H3K4me1_Enh;E052,H3K4me1_Enh;E056,H3K4me1_Enh;E057,H3K4me1_Enh;E080,H3K4me1_Enh;E086,H3K4me1_Enh;E088,H3K4me1_Enh;E113,H3K4me1_Enh;E114,H3K4me1_Enh;E117,H3K4me1_Enh;E119,H3K4me1_Enh;E124,H3K4me1_Enh;E023,H3K4me3_Pro;E030,H3K4me3_Pro;E031,H3K4me3_Pro;E035,H3K4me3_Pro;E109,H3K4me3_Pro;E124,H3K4me3_Pro;E025,H3K9ac_Pro;E029,H3K27ac_Enh;E032,H3K27ac_Enh;E080,H3K27ac_Enh;E113,H3K27ac_Enh;E124,H3K27ac_Enh E006;E021;E029;E046;E080;E086;E088;E117;E120;E124 . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,3.29211855956645e-07;GTEx2015_v6,Artery_Tibial,LRRK2,1.08781866153343e-11;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,1.72128347769633e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,5.31856078341246e-10;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,1.00796507632068e-05;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.06318553434241e-05;Westra2013,Whole_Blood,-,1.3808392059010189E-31;Westra2013,Whole_Blood,LRRK2,2.116806823753094E-5 . . BCL_disc5;HDAC2_disc3 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 7947 . rs11175620 BLD FAT, ESC, BRST, BLD, MUS, ADRL, LNG, CRVX 40610863 40610864 TRUE TRUE FALSE FALSE 0 0 FALSE FALSE FALSE 0.60906 4 G/C 12 40610864 40610864 1 ENSG00000188906 intron_variant NA NA NA NA 1000Genomes,Frequency,gnomAD,TOPMed
rs7294619 LRRK2 12 40617202 0 -0.1276 0.0140 0.8783 0.1217 56306 1417791 0.0382 T C FALSE NA NA 2 1 2 1 1 1 40.61720 3 TRUE 0.75 0 216621 -9.114286 12 40223400 0 0 0 T C 0.11 0.06 0.00 0.11 0 0 E023,7_Enh;E025,7_Enh;E029,1_TssA;E030,2_TssAFlnk;E031,2_TssAFlnk;E032,1_TssA;E033,1_TssA;E035,1_TssA;E046,1_TssA;E050,7_Enh;E051,1_TssA;E062,1_TssA;E063,7_Enh;E066,7_Enh;E068,7_Enh;E074,7_Enh;E076,7_Enh;E078,1_TssA;E086,1_TssA;E103,7_Enh;E116,10_TssBiv;E124,1_TssA E009,23_PromBiv;E023,22_PromP;E025,22_PromP;E029,4_PromD2;E030,3_PromD1;E031,4_PromD2;E032,4_PromD2;E033,4_PromD2;E034,22_PromP;E035,4_PromD2;E036,4_PromD2;E037,22_PromP;E038,4_PromD2;E039,12_TxEnhW;E040,12_TxEnhW;E041,12_TxEnhW;E042,22_PromP;E043,4_PromD2;E044,4_PromD2;E045,12_TxEnhW;E046,4_PromD2;E047,4_PromD2;E048,22_PromP;E050,4_PromD2;E051,4_PromD2;E052,19_DNase;E053,22_PromP;E055,22_PromP;E057,22_PromP;E061,22_PromP;E062,4_PromD2;E063,22_PromP;E066,4_PromD2;E067,22_PromP;E068,22_PromP;E069,22_PromP;E070,22_PromP;E071,12_TxEnhW;E072,22_PromP;E073,22_PromP;E074,19_DNase;E075,22_PromP;E076,4_PromD2;E077,4_PromD2;E078,4_PromD2;E080,22_PromP;E081,22_PromP;E084,22_PromP;E085,22_PromP;E086,22_PromP;E088,22_PromP;E091,22_PromP;E092,22_PromP;E093,22_PromP;E100,22_PromP;E101,4_PromD2;E102,4_PromD2;E103,22_PromP;E106,22_PromP;E108,22_PromP;E109,22_PromP;E110,22_PromP;E111,16_EnhW1;E112,4_PromD2;E113,4_PromD2;E114,22_PromP;E115,23_PromBiv;E116,4_PromD2;E118,22_PromP;E119,22_PromP;E122,22_PromP;E124,3_PromD1 E023,H3K4me1_Enh;E025,H3K4me1_Enh;E026,H3K4me1_Enh;E027,H3K4me1_Enh;E028,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E032,H3K4me1_Enh;E035,H3K4me1_Enh;E036,H3K4me1_Enh;E038,H3K4me1_Enh;E041,H3K4me1_Enh;E043,H3K4me1_Enh;E047,H3K4me1_Enh;E048,H3K4me1_Enh;E049,H3K4me1_Enh;E050,H3K4me1_Enh;E051,H3K4me1_Enh;E052,H3K4me1_Enh;E061,H3K4me1_Enh;E062,H3K4me1_Enh;E063,H3K4me1_Enh;E066,H3K4me1_Enh;E067,H3K4me1_Enh;E068,H3K4me1_Enh;E069,H3K4me1_Enh;E071,H3K4me1_Enh;E072,H3K4me1_Enh;E073,H3K4me1_Enh;E074,H3K4me1_Enh;E076,H3K4me1_Enh;E077,H3K4me1_Enh;E078,H3K4me1_Enh;E080,H3K4me1_Enh;E087,H3K4me1_Enh;E102,H3K4me1_Enh;E103,H3K4me1_Enh;E108,H3K4me1_Enh;E109,H3K4me1_Enh;E111,H3K4me1_Enh;E114,H3K4me1_Enh;E124,H3K4me1_Enh;E129,H3K4me1_Enh;E023,H3K4me3_Pro;E024,H3K4me3_Pro;E025,H3K4me3_Pro;E029,H3K4me3_Pro;E030,H3K4me3_Pro;E031,H3K4me3_Pro;E032,H3K4me3_Pro;E033,H3K4me3_Pro;E035,H3K4me3_Pro;E036,H3K4me3_Pro;E039,H3K4me3_Pro;E041,H3K4me3_Pro;E043,H3K4me3_Pro;E045,H3K4me3_Pro;E046,H3K4me3_Pro;E047,H3K4me3_Pro;E049,H3K4me3_Pro;E051,H3K4me3_Pro;E052,H3K4me3_Pro;E062,H3K4me3_Pro;E063,H3K4me3_Pro;E065,H3K4me3_Pro;E066,H3K4me3_Pro;E067,H3K4me3_Pro;E068,H3K4me3_Pro;E071,H3K4me3_Pro;E072,H3K4me3_Pro;E073,H3K4me3_Pro;E074,H3K4me3_Pro;E076,H3K4me3_Pro;E077,H3K4me3_Pro;E078,H3K4me3_Pro;E084,H3K4me3_Pro;E086,H3K4me3_Pro;E088,H3K4me3_Pro;E091,H3K4me3_Pro;E093,H3K4me3_Pro;E101,H3K4me3_Pro;E102,H3K4me3_Pro;E103,H3K4me3_Pro;E104,H3K4me3_Pro;E105,H3K4me3_Pro;E108,H3K4me3_Pro;E111,H3K4me3_Pro;E112,H3K4me3_Pro;E114,H3K4me3_Pro;E116,H3K4me3_Pro;E124,H3K4me3_Pro;E126,H3K4me3_Pro;E023,H3K9ac_Pro;E025,H3K9ac_Pro;E026,H3K9ac_Pro;E052,H3K9ac_Pro;E062,H3K9ac_Pro;E063,H3K9ac_Pro;E066,H3K9ac_Pro;E068,H3K9ac_Pro;E076,H3K9ac_Pro;E077,H3K9ac_Pro;E086,H3K9ac_Pro;E101,H3K9ac_Pro;E102,H3K9ac_Pro;E116,H3K9ac_Pro;E124,H3K9ac_Pro;E029,H3K27ac_Enh;E032,H3K27ac_Enh;E046,H3K27ac_Enh;E062,H3K27ac_Enh;E063,H3K27ac_Enh;E066,H3K27ac_Enh;E067,H3K27ac_Enh;E068,H3K27ac_Enh;E069,H3K27ac_Enh;E072,H3K27ac_Enh;E073,H3K27ac_Enh;E074,H3K27ac_Enh;E075,H3K27ac_Enh;E076,H3K27ac_Enh;E078,H3K27ac_Enh;E084,H3K27ac_Enh;E093,H3K27ac_Enh;E101,H3K27ac_Enh;E102,H3K27ac_Enh;E103,H3K27ac_Enh;E116,H3K27ac_Enh;E124,H3K27ac_Enh;E126,H3K27ac_Enh . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,4.21086496303076e-07;GTEx2015_v6,Artery_Tibial,LRRK2,7.12887180198536e-12;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,1.24729820163706e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,5.97959499940652e-10;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,1.00796507632068e-05;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.08361107066017e-05;Westra2013,Whole_Blood,-,1.9330946764156724E-31;Westra2013,Whole_Blood,LRRK2,1.807765948958669E-5 . . Barx1;Barx2;CDP_2;En-1_1;Hoxb6;Irf_known7;Ncx_1;Pou5f1_known2;Sox_18;Sox_3;Sox_9 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 1609 . rs7294619 BLD, GI, KID FAT, BLD, LIV, BRN, GI 40617201 40617202 FALSE TRUE FALSE FALSE 0 0.939999997615814 TRUE FALSE FALSE 0.07617 5 T/C 12 40617202 40617202 1 ENSG00000225342 non_coding_transcript_variant NA NA NA NA regulatory_region_variant 1000Genomes,Cited,Frequency,gnomAD,TOPMed
rs7294619 LRRK2 12 40617202 0 -0.1276 0.0140 0.8783 0.1217 56306 1417791 0.0382 T C FALSE NA NA 2 1 2 1 1 1 40.61720 3 TRUE 0.75 0 216621 -9.114286 12 40223400 0 0 0 T C 0.11 0.06 0.00 0.11 0 0 E023,7_Enh;E025,7_Enh;E029,1_TssA;E030,2_TssAFlnk;E031,2_TssAFlnk;E032,1_TssA;E033,1_TssA;E035,1_TssA;E046,1_TssA;E050,7_Enh;E051,1_TssA;E062,1_TssA;E063,7_Enh;E066,7_Enh;E068,7_Enh;E074,7_Enh;E076,7_Enh;E078,1_TssA;E086,1_TssA;E103,7_Enh;E116,10_TssBiv;E124,1_TssA E009,23_PromBiv;E023,22_PromP;E025,22_PromP;E029,4_PromD2;E030,3_PromD1;E031,4_PromD2;E032,4_PromD2;E033,4_PromD2;E034,22_PromP;E035,4_PromD2;E036,4_PromD2;E037,22_PromP;E038,4_PromD2;E039,12_TxEnhW;E040,12_TxEnhW;E041,12_TxEnhW;E042,22_PromP;E043,4_PromD2;E044,4_PromD2;E045,12_TxEnhW;E046,4_PromD2;E047,4_PromD2;E048,22_PromP;E050,4_PromD2;E051,4_PromD2;E052,19_DNase;E053,22_PromP;E055,22_PromP;E057,22_PromP;E061,22_PromP;E062,4_PromD2;E063,22_PromP;E066,4_PromD2;E067,22_PromP;E068,22_PromP;E069,22_PromP;E070,22_PromP;E071,12_TxEnhW;E072,22_PromP;E073,22_PromP;E074,19_DNase;E075,22_PromP;E076,4_PromD2;E077,4_PromD2;E078,4_PromD2;E080,22_PromP;E081,22_PromP;E084,22_PromP;E085,22_PromP;E086,22_PromP;E088,22_PromP;E091,22_PromP;E092,22_PromP;E093,22_PromP;E100,22_PromP;E101,4_PromD2;E102,4_PromD2;E103,22_PromP;E106,22_PromP;E108,22_PromP;E109,22_PromP;E110,22_PromP;E111,16_EnhW1;E112,4_PromD2;E113,4_PromD2;E114,22_PromP;E115,23_PromBiv;E116,4_PromD2;E118,22_PromP;E119,22_PromP;E122,22_PromP;E124,3_PromD1 E023,H3K4me1_Enh;E025,H3K4me1_Enh;E026,H3K4me1_Enh;E027,H3K4me1_Enh;E028,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E032,H3K4me1_Enh;E035,H3K4me1_Enh;E036,H3K4me1_Enh;E038,H3K4me1_Enh;E041,H3K4me1_Enh;E043,H3K4me1_Enh;E047,H3K4me1_Enh;E048,H3K4me1_Enh;E049,H3K4me1_Enh;E050,H3K4me1_Enh;E051,H3K4me1_Enh;E052,H3K4me1_Enh;E061,H3K4me1_Enh;E062,H3K4me1_Enh;E063,H3K4me1_Enh;E066,H3K4me1_Enh;E067,H3K4me1_Enh;E068,H3K4me1_Enh;E069,H3K4me1_Enh;E071,H3K4me1_Enh;E072,H3K4me1_Enh;E073,H3K4me1_Enh;E074,H3K4me1_Enh;E076,H3K4me1_Enh;E077,H3K4me1_Enh;E078,H3K4me1_Enh;E080,H3K4me1_Enh;E087,H3K4me1_Enh;E102,H3K4me1_Enh;E103,H3K4me1_Enh;E108,H3K4me1_Enh;E109,H3K4me1_Enh;E111,H3K4me1_Enh;E114,H3K4me1_Enh;E124,H3K4me1_Enh;E129,H3K4me1_Enh;E023,H3K4me3_Pro;E024,H3K4me3_Pro;E025,H3K4me3_Pro;E029,H3K4me3_Pro;E030,H3K4me3_Pro;E031,H3K4me3_Pro;E032,H3K4me3_Pro;E033,H3K4me3_Pro;E035,H3K4me3_Pro;E036,H3K4me3_Pro;E039,H3K4me3_Pro;E041,H3K4me3_Pro;E043,H3K4me3_Pro;E045,H3K4me3_Pro;E046,H3K4me3_Pro;E047,H3K4me3_Pro;E049,H3K4me3_Pro;E051,H3K4me3_Pro;E052,H3K4me3_Pro;E062,H3K4me3_Pro;E063,H3K4me3_Pro;E065,H3K4me3_Pro;E066,H3K4me3_Pro;E067,H3K4me3_Pro;E068,H3K4me3_Pro;E071,H3K4me3_Pro;E072,H3K4me3_Pro;E073,H3K4me3_Pro;E074,H3K4me3_Pro;E076,H3K4me3_Pro;E077,H3K4me3_Pro;E078,H3K4me3_Pro;E084,H3K4me3_Pro;E086,H3K4me3_Pro;E088,H3K4me3_Pro;E091,H3K4me3_Pro;E093,H3K4me3_Pro;E101,H3K4me3_Pro;E102,H3K4me3_Pro;E103,H3K4me3_Pro;E104,H3K4me3_Pro;E105,H3K4me3_Pro;E108,H3K4me3_Pro;E111,H3K4me3_Pro;E112,H3K4me3_Pro;E114,H3K4me3_Pro;E116,H3K4me3_Pro;E124,H3K4me3_Pro;E126,H3K4me3_Pro;E023,H3K9ac_Pro;E025,H3K9ac_Pro;E026,H3K9ac_Pro;E052,H3K9ac_Pro;E062,H3K9ac_Pro;E063,H3K9ac_Pro;E066,H3K9ac_Pro;E068,H3K9ac_Pro;E076,H3K9ac_Pro;E077,H3K9ac_Pro;E086,H3K9ac_Pro;E101,H3K9ac_Pro;E102,H3K9ac_Pro;E116,H3K9ac_Pro;E124,H3K9ac_Pro;E029,H3K27ac_Enh;E032,H3K27ac_Enh;E046,H3K27ac_Enh;E062,H3K27ac_Enh;E063,H3K27ac_Enh;E066,H3K27ac_Enh;E067,H3K27ac_Enh;E068,H3K27ac_Enh;E069,H3K27ac_Enh;E072,H3K27ac_Enh;E073,H3K27ac_Enh;E074,H3K27ac_Enh;E075,H3K27ac_Enh;E076,H3K27ac_Enh;E078,H3K27ac_Enh;E084,H3K27ac_Enh;E093,H3K27ac_Enh;E101,H3K27ac_Enh;E102,H3K27ac_Enh;E103,H3K27ac_Enh;E116,H3K27ac_Enh;E124,H3K27ac_Enh;E126,H3K27ac_Enh . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,4.21086496303076e-07;GTEx2015_v6,Artery_Tibial,LRRK2,7.12887180198536e-12;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,1.24729820163706e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,5.97959499940652e-10;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,1.00796507632068e-05;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.08361107066017e-05;Westra2013,Whole_Blood,-,1.9330946764156724E-31;Westra2013,Whole_Blood,LRRK2,1.807765948958669E-5 . . Barx1;Barx2;CDP_2;En-1_1;Hoxb6;Irf_known7;Ncx_1;Pou5f1_known2;Sox_18;Sox_3;Sox_9 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 1609 . rs7294619 BLD, GI, KID FAT, BLD, LIV, BRN, GI 40617201 40617202 FALSE TRUE FALSE FALSE 0 0.939999997615814 TRUE FALSE FALSE 0.07617 5 T/C 12 40617202 40617202 1 ENSG00000225342 intron_variant NA NA NA NA regulatory_region_variant 1000Genomes,Cited,Frequency,gnomAD,TOPMed
rs7294619 LRRK2 12 40617202 0 -0.1276 0.0140 0.8783 0.1217 56306 1417791 0.0382 T C FALSE NA NA 2 1 2 1 1 1 40.61720 3 TRUE 0.75 0 216621 -9.114286 12 40223400 0 0 0 T C 0.11 0.06 0.00 0.11 0 0 E023,7_Enh;E025,7_Enh;E029,1_TssA;E030,2_TssAFlnk;E031,2_TssAFlnk;E032,1_TssA;E033,1_TssA;E035,1_TssA;E046,1_TssA;E050,7_Enh;E051,1_TssA;E062,1_TssA;E063,7_Enh;E066,7_Enh;E068,7_Enh;E074,7_Enh;E076,7_Enh;E078,1_TssA;E086,1_TssA;E103,7_Enh;E116,10_TssBiv;E124,1_TssA E009,23_PromBiv;E023,22_PromP;E025,22_PromP;E029,4_PromD2;E030,3_PromD1;E031,4_PromD2;E032,4_PromD2;E033,4_PromD2;E034,22_PromP;E035,4_PromD2;E036,4_PromD2;E037,22_PromP;E038,4_PromD2;E039,12_TxEnhW;E040,12_TxEnhW;E041,12_TxEnhW;E042,22_PromP;E043,4_PromD2;E044,4_PromD2;E045,12_TxEnhW;E046,4_PromD2;E047,4_PromD2;E048,22_PromP;E050,4_PromD2;E051,4_PromD2;E052,19_DNase;E053,22_PromP;E055,22_PromP;E057,22_PromP;E061,22_PromP;E062,4_PromD2;E063,22_PromP;E066,4_PromD2;E067,22_PromP;E068,22_PromP;E069,22_PromP;E070,22_PromP;E071,12_TxEnhW;E072,22_PromP;E073,22_PromP;E074,19_DNase;E075,22_PromP;E076,4_PromD2;E077,4_PromD2;E078,4_PromD2;E080,22_PromP;E081,22_PromP;E084,22_PromP;E085,22_PromP;E086,22_PromP;E088,22_PromP;E091,22_PromP;E092,22_PromP;E093,22_PromP;E100,22_PromP;E101,4_PromD2;E102,4_PromD2;E103,22_PromP;E106,22_PromP;E108,22_PromP;E109,22_PromP;E110,22_PromP;E111,16_EnhW1;E112,4_PromD2;E113,4_PromD2;E114,22_PromP;E115,23_PromBiv;E116,4_PromD2;E118,22_PromP;E119,22_PromP;E122,22_PromP;E124,3_PromD1 E023,H3K4me1_Enh;E025,H3K4me1_Enh;E026,H3K4me1_Enh;E027,H3K4me1_Enh;E028,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E032,H3K4me1_Enh;E035,H3K4me1_Enh;E036,H3K4me1_Enh;E038,H3K4me1_Enh;E041,H3K4me1_Enh;E043,H3K4me1_Enh;E047,H3K4me1_Enh;E048,H3K4me1_Enh;E049,H3K4me1_Enh;E050,H3K4me1_Enh;E051,H3K4me1_Enh;E052,H3K4me1_Enh;E061,H3K4me1_Enh;E062,H3K4me1_Enh;E063,H3K4me1_Enh;E066,H3K4me1_Enh;E067,H3K4me1_Enh;E068,H3K4me1_Enh;E069,H3K4me1_Enh;E071,H3K4me1_Enh;E072,H3K4me1_Enh;E073,H3K4me1_Enh;E074,H3K4me1_Enh;E076,H3K4me1_Enh;E077,H3K4me1_Enh;E078,H3K4me1_Enh;E080,H3K4me1_Enh;E087,H3K4me1_Enh;E102,H3K4me1_Enh;E103,H3K4me1_Enh;E108,H3K4me1_Enh;E109,H3K4me1_Enh;E111,H3K4me1_Enh;E114,H3K4me1_Enh;E124,H3K4me1_Enh;E129,H3K4me1_Enh;E023,H3K4me3_Pro;E024,H3K4me3_Pro;E025,H3K4me3_Pro;E029,H3K4me3_Pro;E030,H3K4me3_Pro;E031,H3K4me3_Pro;E032,H3K4me3_Pro;E033,H3K4me3_Pro;E035,H3K4me3_Pro;E036,H3K4me3_Pro;E039,H3K4me3_Pro;E041,H3K4me3_Pro;E043,H3K4me3_Pro;E045,H3K4me3_Pro;E046,H3K4me3_Pro;E047,H3K4me3_Pro;E049,H3K4me3_Pro;E051,H3K4me3_Pro;E052,H3K4me3_Pro;E062,H3K4me3_Pro;E063,H3K4me3_Pro;E065,H3K4me3_Pro;E066,H3K4me3_Pro;E067,H3K4me3_Pro;E068,H3K4me3_Pro;E071,H3K4me3_Pro;E072,H3K4me3_Pro;E073,H3K4me3_Pro;E074,H3K4me3_Pro;E076,H3K4me3_Pro;E077,H3K4me3_Pro;E078,H3K4me3_Pro;E084,H3K4me3_Pro;E086,H3K4me3_Pro;E088,H3K4me3_Pro;E091,H3K4me3_Pro;E093,H3K4me3_Pro;E101,H3K4me3_Pro;E102,H3K4me3_Pro;E103,H3K4me3_Pro;E104,H3K4me3_Pro;E105,H3K4me3_Pro;E108,H3K4me3_Pro;E111,H3K4me3_Pro;E112,H3K4me3_Pro;E114,H3K4me3_Pro;E116,H3K4me3_Pro;E124,H3K4me3_Pro;E126,H3K4me3_Pro;E023,H3K9ac_Pro;E025,H3K9ac_Pro;E026,H3K9ac_Pro;E052,H3K9ac_Pro;E062,H3K9ac_Pro;E063,H3K9ac_Pro;E066,H3K9ac_Pro;E068,H3K9ac_Pro;E076,H3K9ac_Pro;E077,H3K9ac_Pro;E086,H3K9ac_Pro;E101,H3K9ac_Pro;E102,H3K9ac_Pro;E116,H3K9ac_Pro;E124,H3K9ac_Pro;E029,H3K27ac_Enh;E032,H3K27ac_Enh;E046,H3K27ac_Enh;E062,H3K27ac_Enh;E063,H3K27ac_Enh;E066,H3K27ac_Enh;E067,H3K27ac_Enh;E068,H3K27ac_Enh;E069,H3K27ac_Enh;E072,H3K27ac_Enh;E073,H3K27ac_Enh;E074,H3K27ac_Enh;E075,H3K27ac_Enh;E076,H3K27ac_Enh;E078,H3K27ac_Enh;E084,H3K27ac_Enh;E093,H3K27ac_Enh;E101,H3K27ac_Enh;E102,H3K27ac_Enh;E103,H3K27ac_Enh;E116,H3K27ac_Enh;E124,H3K27ac_Enh;E126,H3K27ac_Enh . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,4.21086496303076e-07;GTEx2015_v6,Artery_Tibial,LRRK2,7.12887180198536e-12;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,1.24729820163706e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,5.97959499940652e-10;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,1.00796507632068e-05;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.08361107066017e-05;Westra2013,Whole_Blood,-,1.9330946764156724E-31;Westra2013,Whole_Blood,LRRK2,1.807765948958669E-5 . . Barx1;Barx2;CDP_2;En-1_1;Hoxb6;Irf_known7;Ncx_1;Pou5f1_known2;Sox_18;Sox_3;Sox_9 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 1609 . rs7294619 BLD, GI, KID FAT, BLD, LIV, BRN, GI 40617201 40617202 FALSE TRUE FALSE FALSE 0 0.939999997615814 TRUE FALSE FALSE 0.07617 5 T/C 12 40617202 40617202 1 ENSG00000188906 intron_variant NA NA NA NA regulatory_region_variant 1000Genomes,Cited,Frequency,gnomAD,TOPMed
rs74324737 LRRK2 12 40625081 0 0.1246 0.0141 0.1216 0.1216 56306 1417791 0.0382 A G FALSE NA NA 4 1 4 1 NA NA 40.62508 2 TRUE 0.50 0 216621 8.836879 12 40231279 0 0 0 G A 0.09 0.06 0.00 0.11 0 0 E029,6_EnhG;E030,6_EnhG;E031,7_Enh;E032,6_EnhG;E080,7_Enh;E124,6_EnhG E029,10_TxEnh5;E030,10_TxEnh5;E031,10_TxEnh5;E032,10_TxEnh5;E124,10_TxEnh5 E029,H3K27ac_Enh;E032,H3K27ac_Enh;E046,H3K27ac_Enh;E068,H3K27ac_Enh;E080,H3K27ac_Enh;E124,H3K27ac_Enh;E029,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E032,H3K4me1_Enh;E067,H3K4me1_Enh;E073,H3K4me1_Enh;E078,H3K4me1_Enh;E116,H3K4me1_Enh;E124,H3K4me1_Enh;E031,H3K4me3_Pro;E067,H3K4me3_Pro;E116,H3K4me3_Pro;E124,H3K4me3_Pro;E124,H3K9ac_Pro . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,7.71727072375557e-07;GTEx2015_v6,Artery_Tibial,LRRK2,3.79436480774191e-12;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,6.94075809560474e-06;GTEx2015_v6,Nerve_Tibial,LRRK2,8.74398504351068e-10;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,9.31129758632871e-06;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.18501232307152e-05 . . E2A_3;E2A_5;Lmo2-complex_1;Mtf1_1;Myf_1;Myf_3;NF-E2_disc3;TCF12_disc1;ZEB1_known3 ENSG00000188906.9 LRRK2 0 0 NM_198578 LRRK2 0 0 INT rs74324737 BLD, ADRL 40625080 40625081 FALSE TRUE FALSE FALSE 0 1.79999995231628 TRUE FALSE FALSE 0.9223 5 G/A 12 40625081 40625081 1 ENSG00000188906 intron_variant NA NA NA NA 1000Genomes,Cited,Frequency,gnomAD,TOPMed
rs74324737 LRRK2 12 40625081 0 0.1246 0.0141 0.1216 0.1216 56306 1417791 0.0382 A G FALSE NA NA 4 1 4 1 NA NA 40.62508 2 TRUE 0.50 0 216621 8.836879 12 40231279 0 0 0 G A 0.09 0.06 0.00 0.11 0 0 E029,6_EnhG;E030,6_EnhG;E031,7_Enh;E032,6_EnhG;E080,7_Enh;E124,6_EnhG E029,10_TxEnh5;E030,10_TxEnh5;E031,10_TxEnh5;E032,10_TxEnh5;E124,10_TxEnh5 E029,H3K27ac_Enh;E032,H3K27ac_Enh;E046,H3K27ac_Enh;E068,H3K27ac_Enh;E080,H3K27ac_Enh;E124,H3K27ac_Enh;E029,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E032,H3K4me1_Enh;E067,H3K4me1_Enh;E073,H3K4me1_Enh;E078,H3K4me1_Enh;E116,H3K4me1_Enh;E124,H3K4me1_Enh;E031,H3K4me3_Pro;E067,H3K4me3_Pro;E116,H3K4me3_Pro;E124,H3K4me3_Pro;E124,H3K9ac_Pro . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,7.71727072375557e-07;GTEx2015_v6,Artery_Tibial,LRRK2,3.79436480774191e-12;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,6.94075809560474e-06;GTEx2015_v6,Nerve_Tibial,LRRK2,8.74398504351068e-10;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,9.31129758632871e-06;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.18501232307152e-05 . . E2A_3;E2A_5;Lmo2-complex_1;Mtf1_1;Myf_1;Myf_3;NF-E2_disc3;TCF12_disc1;ZEB1_known3 ENSG00000188906.9 LRRK2 0 0 NM_198578 LRRK2 0 0 INT rs74324737 BLD, ADRL 40625080 40625081 FALSE TRUE FALSE FALSE 0 1.79999995231628 TRUE FALSE FALSE 0.9223 5 G/A 12 40625081 40625081 1 ENSG00000188906 non_coding_transcript_variant NA NA NA NA 1000Genomes,Cited,Frequency,gnomAD,TOPMed
rs76904798 LRRK2 12 40614434 0 0.1439 0.0130 0.1444 0.1444 56306 1417791 0.0382 T C TRUE NA NA 1 1 1 1 1 1 40.61443 3 TRUE 0.75 0 216621 11.069231 12 40220632 0 0 0 C T 0.11 0.21 0.03 0.13 0 0 E029,7_Enh;E030,7_Enh;E124,7_Enh E029,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E124,H3K4me1_Enh;E124,H3K27ac_Enh . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,2.6136557196757e-09;GTEx2015_v6,Artery_Coronary,LRRK2,8.10828434519411e-08;GTEx2015_v6,Artery_Tibial,LRRK2,1.29589062525083e-14;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,2.01546552400868e-05;GTEx2015_v6,Esophagus_Muscularis,LRRK2,1.17034509288903e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,1.17833931025132e-15;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,3.02678179339592e-06;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.21658440247309e-07 25064009,Parkinson’s disease,5E-14 . Dbx1;Hmx_2;Hoxb8;Hoxd8;Ncx_2;Nkx6-1_3;Pou2f2_known2;Sox_14;Sox_15;Sox_16;Sox_18;Sox_19;Sox_2;Sox_5;Sox_7;Sox_9 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 4377 . rs76904798 BLD 40614433 40614434 FALSE FALSE FALSE FALSE 0 0.230000004172325 TRUE FALSE FALSE 0.14464 6 C/T 12 40614434 40614434 1 ENSG00000225342 non_coding_transcript_variant NA NA NA NA 1000Genomes,Cited,Frequency,gnomAD,Phenotype_or_Disease,TOPMed
rs76904798 LRRK2 12 40614434 0 0.1439 0.0130 0.1444 0.1444 56306 1417791 0.0382 T C TRUE NA NA 1 1 1 1 1 1 40.61443 3 TRUE 0.75 0 216621 11.069231 12 40220632 0 0 0 C T 0.11 0.21 0.03 0.13 0 0 E029,7_Enh;E030,7_Enh;E124,7_Enh E029,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E124,H3K4me1_Enh;E124,H3K27ac_Enh . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,2.6136557196757e-09;GTEx2015_v6,Artery_Coronary,LRRK2,8.10828434519411e-08;GTEx2015_v6,Artery_Tibial,LRRK2,1.29589062525083e-14;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,2.01546552400868e-05;GTEx2015_v6,Esophagus_Muscularis,LRRK2,1.17034509288903e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,1.17833931025132e-15;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,3.02678179339592e-06;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.21658440247309e-07 25064009,Parkinson’s disease,5E-14 . Dbx1;Hmx_2;Hoxb8;Hoxd8;Ncx_2;Nkx6-1_3;Pou2f2_known2;Sox_14;Sox_15;Sox_16;Sox_18;Sox_19;Sox_2;Sox_5;Sox_7;Sox_9 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 4377 . rs76904798 BLD 40614433 40614434 FALSE FALSE FALSE FALSE 0 0.230000004172325 TRUE FALSE FALSE 0.14464 6 C/T 12 40614434 40614434 1 ENSG00000225342 intron_variant NA NA NA NA 1000Genomes,Cited,Frequency,gnomAD,Phenotype_or_Disease,TOPMed
rs76904798 LRRK2 12 40614434 0 0.1439 0.0130 0.1444 0.1444 56306 1417791 0.0382 T C TRUE NA NA 1 1 1 1 1 1 40.61443 3 TRUE 0.75 0 216621 11.069231 12 40220632 0 0 0 C T 0.11 0.21 0.03 0.13 0 0 E029,7_Enh;E030,7_Enh;E124,7_Enh E029,H3K4me1_Enh;E030,H3K4me1_Enh;E031,H3K4me1_Enh;E124,H3K4me1_Enh;E124,H3K27ac_Enh . GTEx2015_v6,Adipose_Subcutaneous,LRRK2,2.6136557196757e-09;GTEx2015_v6,Artery_Coronary,LRRK2,8.10828434519411e-08;GTEx2015_v6,Artery_Tibial,LRRK2,1.29589062525083e-14;GTEx2015_v6,Cells_Transformed_fibroblasts,LRRK2,2.01546552400868e-05;GTEx2015_v6,Esophagus_Muscularis,LRRK2,1.17034509288903e-05;GTEx2015_v6,Nerve_Tibial,LRRK2,1.17833931025132e-15;GTEx2015_v6,Skin_Not_Sun_Exposed_Suprapubic,LRRK2,3.02678179339592e-06;GTEx2015_v6,Skin_Sun_Exposed_Lower_leg,LRRK2,1.21658440247309e-07 25064009,Parkinson’s disease,5E-14 . Dbx1;Hmx_2;Hoxb8;Hoxd8;Ncx_2;Nkx6-1_3;Pou2f2_known2;Sox_14;Sox_15;Sox_16;Sox_18;Sox_19;Sox_2;Sox_5;Sox_7;Sox_9 ENSG00000225342.1 AC079630.4 0 0 NM_198578 LRRK2 5 4377 . rs76904798 BLD 40614433 40614434 FALSE FALSE FALSE FALSE 0 0.230000004172325 TRUE FALSE FALSE 0.14464 6 C/T 12 40614434 40614434 1 ENSG00000188906 intron_variant NA NA NA NA 1000Genomes,Cited,Frequency,gnomAD,Phenotype_or_Disease,TOPMed

Summary plots

Credible Set bin plot 

gg_cs_bin <- echoannot::CS_bin_plot(merged_DT = merged_DT,
                                    show_plot = FALSE)

Credible Set counts plot 

gg_cs_counts <- echoannot::CS_counts_plot(merged_DT = merged_DT, 
                                          show_plot = FALSE)

Epigenomic data 

gg_epi <- echoannot::peak_overlap_plot(
    merged_DT = merged_DT, 
    include.NOTT2019_enhancers_promoters = TRUE,
    include.NOTT2019_PLACseq = TRUE,
    #### Omit many annotations to save time ####
    include.NOTT2019_peaks = FALSE,
    include.CORCES2020_scATACpeaks = FALSE, 
    include.CORCES2020_Cicero_coaccess = FALSE, 
    include.CORCES2020_bulkATACpeaks = FALSE, 
    include.CORCES2020_HiChIP_FitHiChIP_coaccess = FALSE,
    include.CORCES2020_gene_annotations = FALSE)
## ++ NOTT2019:: Getting regulatory regions data.
## Importing Astrocyte enhancers ...
## Importing Astrocyte promoters ...
## Importing Neuronal enhancers ...
## Importing Neuronal promoters ...
## Importing Oligo enhancers ...
## Importing Oligo promoters ...
## Importing Microglia enhancers ...
## Importing Microglia promoters ...
## Converting dat to GRanges object.
## Converting dat to GRanges object.
## 48 query SNP(s) detected with reference overlap.
## ++ NOTT2019:: Getting interaction anchors data.
## Importing Microglia interactome ...
## Importing Neuronal interactome ...
## Importing Oligo interactome ...
## Converting dat to GRanges object.
## 52 query SNP(s) detected with reference overlap.
## Converting dat to GRanges object.
## 44 query SNP(s) detected with reference overlap.
## Found more than one class "simpleUnit" in cache; using the first, from namespace 'hexbin'
## Also defined by 'ggbio'

Super summary plot

Creates one big merged plot using the subfunctions above.

super_plot <- echoannot::super_summary_plot(merged_DT = merged_DT, 
                                            plot_missense = FALSE)

Session Info 

utils::sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] echoannot_0.99.10 BiocStyle_2.25.0 
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2                  reticulate_1.26            
##   [3] R.utils_2.12.0              RUnit_0.4.32               
##   [5] tidyselect_1.2.0            RSQLite_2.2.18             
##   [7] AnnotationDbi_1.59.1        htmlwidgets_1.5.4          
##   [9] grid_4.2.1                  BiocParallel_1.31.15       
##  [11] XGR_1.1.8                   munsell_0.5.0              
##  [13] codetools_0.2-18            ragg_1.2.4                 
##  [15] interp_1.1-3                DT_0.26                    
##  [17] withr_2.5.0                 colorspace_2.0-3           
##  [19] OrganismDbi_1.39.1          Biobase_2.57.3             
##  [21] filelock_1.0.2              highr_0.9                  
##  [23] knitr_1.40                  supraHex_1.35.0            
##  [25] rstudioapi_0.14             stats4_4.2.1               
##  [27] DescTools_0.99.47           labeling_0.4.2             
##  [29] MatrixGenerics_1.9.1        GenomeInfoDbData_1.2.9     
##  [31] farver_2.1.1                bit64_4.0.5                
##  [33] echoconda_0.99.7            rprojroot_2.0.3            
##  [35] basilisk_1.9.12             vctrs_0.5.0                
##  [37] generics_0.1.3              xfun_0.34                  
##  [39] biovizBase_1.45.0           BiocFileCache_2.5.2        
##  [41] R6_2.5.1                    GenomeInfoDb_1.33.16       
##  [43] RJSONIO_1.3-1.6             AnnotationFilter_1.21.0    
##  [45] bitops_1.0-7                cachem_1.0.6               
##  [47] reshape_0.8.9               DelayedArray_0.23.2        
##  [49] assertthat_0.2.1            BiocIO_1.7.1               
##  [51] scales_1.2.1                nnet_7.3-18                
##  [53] rootSolve_1.8.2.3           gtable_0.3.1               
##  [55] lmom_2.9                    ggbio_1.45.0               
##  [57] ensembldb_2.21.5            rlang_1.0.6                
##  [59] systemfonts_1.0.4           echodata_0.99.15           
##  [61] splines_4.2.1               lazyeval_0.2.2             
##  [63] rtracklayer_1.57.0          dichromat_2.0-0.1          
##  [65] hexbin_1.28.2               checkmate_2.1.0            
##  [67] BiocManager_1.30.19         yaml_2.3.6                 
##  [69] reshape2_1.4.4              backports_1.4.1            
##  [71] GenomicFeatures_1.49.8      ggnetwork_0.5.10           
##  [73] Hmisc_4.7-1                 RBGL_1.73.0                
##  [75] tools_4.2.1                 bookdown_0.29              
##  [77] ggplot2_3.3.6               ellipsis_0.3.2             
##  [79] jquerylib_0.1.4             RColorBrewer_1.1-3         
##  [81] proxy_0.4-27                BiocGenerics_0.43.4        
##  [83] Rcpp_1.0.9                  plyr_1.8.7                 
##  [85] base64enc_0.1-3             progress_1.2.2             
##  [87] zlibbioc_1.43.0             purrr_0.3.5                
##  [89] RCurl_1.98-1.9              basilisk.utils_1.9.4       
##  [91] prettyunits_1.1.1           rpart_4.1.16               
##  [93] deldir_1.0-6                S4Vectors_0.35.4           
##  [95] cluster_2.1.4               SummarizedExperiment_1.27.3
##  [97] ggrepel_0.9.1               fs_1.5.2                   
##  [99] crul_1.3                    magrittr_2.0.3             
## [101] data.table_1.14.4           echotabix_0.99.8           
## [103] dnet_1.1.7                  openxlsx_4.2.5.1           
## [105] mvtnorm_1.1-3               ProtGenerics_1.29.1        
## [107] matrixStats_0.62.0          patchwork_1.1.2            
## [109] hms_1.1.2                   evaluate_0.17              
## [111] XML_3.99-0.11               jpeg_0.1-9                 
## [113] readxl_1.4.1                IRanges_2.31.2             
## [115] gridExtra_2.3               compiler_4.2.1             
## [117] biomaRt_2.53.3              tibble_3.1.8               
## [119] haploR_4.0.6                crayon_1.5.2               
## [121] R.oo_1.25.0                 htmltools_0.5.3            
## [123] tzdb_0.3.0                  Formula_1.2-4              
## [125] tidyr_1.2.1                 expm_0.999-6               
## [127] Exact_3.2                   DBI_1.1.3                  
## [129] dbplyr_2.2.1                MASS_7.3-58.1              
## [131] rappdirs_0.3.3              boot_1.3-28                
## [133] Matrix_1.5-1                readr_2.1.3                
## [135] piggyback_0.1.4             cli_3.4.1                  
## [137] R.methodsS3_1.8.2           parallel_4.2.1             
## [139] igraph_1.3.5                GenomicRanges_1.49.1       
## [141] pkgconfig_2.0.3             pkgdown_2.0.6.9000         
## [143] GenomicAlignments_1.33.1    dir.expiry_1.5.1           
## [145] RCircos_1.2.2               foreign_0.8-83             
## [147] osfr_0.2.9                  xml2_1.3.3                 
## [149] bslib_0.4.0                 XVector_0.37.1             
## [151] stringr_1.4.1               VariantAnnotation_1.43.3   
## [153] digest_0.6.30               graph_1.75.1               
## [155] httpcode_0.3.0              Biostrings_2.65.6          
## [157] rmarkdown_2.17              cellranger_1.1.0           
## [159] htmlTable_2.4.1             gld_2.6.6                  
## [161] restfulr_0.0.15             curl_4.3.3                 
## [163] Rsamtools_2.13.4            rjson_0.2.21               
## [165] lifecycle_1.0.3             nlme_3.1-160               
## [167] jsonlite_1.8.3              viridisLite_0.4.1          
## [169] desc_1.4.2                  BSgenome_1.65.4            
## [171] fansi_1.0.3                 downloadR_0.99.5           
## [173] pillar_1.8.1                lattice_0.20-45            
## [175] GGally_2.1.2                KEGGREST_1.37.3            
## [177] fastmap_1.1.0               httr_1.4.4                 
## [179] survival_3.4-0              glue_1.6.2                 
## [181] zip_2.2.2                   png_0.1-7                  
## [183] bit_4.0.4                   Rgraphviz_2.41.2           
## [185] class_7.3-20                stringi_1.7.8              
## [187] sass_0.4.2                  blob_1.2.3                 
## [189] textshaping_0.3.6           latticeExtra_0.6-30        
## [191] memoise_2.0.1               dplyr_1.0.10               
## [193] e1071_1.7-12                ape_5.6-2