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Table 2 Annotated transcript and SNP table

From: Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test

Transcript

Gene

Chromosome

Start

Length

SNP

DBSnp rs

SNP annotation

GI_42544126-I

SF1

chr11

64532075

14241

11_64511322

rs2073798

RASGRP2 intron

11_64519345

rs686171

PYGM intron

11_64546106

rs3741398

SF1 2 kb upstream, nc transcript variant, 5’ UTR

11_64546257

rs1633462

SF1 2 kb upstream, nc transcript variant, 5’ UTR

11_64573589

rs669976

MEN1 intron

11_64576598

rs67808744

MEN1 intron

11_64577620

rs7949944

MEN1 5’ UTR, 2 kb upstream

GI_23097237-S

CHST13

chr3

126243130

19004

3_126218788

rs6774768

UROC1 intron

3_126228953

rs1873388

UROC1 intron

3_126242964

rs1388096

CHST13 2 kb upstream

3_126245956

rs4592980

CHST13 intron/3’UTR

3_126246370

rs1994642

CHST13 intron/3’UTR

3_126247795

rs11717719

CHST13 intron

3_126247848

rs11718493

CHST13 intron

GI_10863968-S

POLD4

chr11

67119018

2034

11_67196237

rs1476792

 

Hs.283934-S

TSPAN16

chr19

11406815

30857

19_11340057

rs17001244

 

19_11358700

rs4804579

 

19_11374675

rs416231

 

19_11380295

rs4804159

 

19_11406952

rs374409

 

GI_12056480-A

UTS2

chr1

7907271

6280

1_7710810

rs58905635

CAMTA1 intron

1_7725855

rs4908471

CAMTA1 intron

1_7749807

rs3124797

CAMTA1 intron

GI_20986517-S

MAPK8IP1

chr11

45907046

20970

11_45838926

rs11038668

 

11_45840939

rs7112505

 

11_45891418

rs7123390

CRY2 intron

Hs.58104-S

FAM101B

chr17

289771

8960

17_185027

rs12951437

 

17_198698

rs11869174

 

17_206962

rs11657163

 

GI_41393558-I

KIF1B

chr1

10270763

97892

1_10270386

rs3828081

KIF1B 2 kb upstream

1_10307453

rs4240911

KIF1B intron

1_10438687

rs1536262

KIF1B 3’UTR

GI_4506738-S

RPS6KB2

chr11

67195934

6945

11_67196237

rs1476792

RPS6KB2 intron

11_67204342

rs12787021

PTPRCAP intron

11_67213956

rs2109123

 

11_67253564

rs7110021

 

11_67258805

rs751567

 

11_67264679

rs2276120

 

GI_15451941-S

UBA52

chr19

18682613

5657

19_18499151

rs1059022

 

19_18499238

rs1804826

 

19_18715154

rs72995445

CRLF1 intron

19_18859680

rs11085244

 
  1. Gene symbols and coordinates for the ten transcripts that were detected as being potentially cis-regulated by SNPs in our covariance kernel. The closest SNPs to each gene are listed