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Table 1 T1D 3DFAACTS SNPs identified using the 3DFAACTS-SNP filtering workflow from T1D fine-mapping SNPs

From: 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk

Chromosome

Position

SNP id

Nearest locus (linear distance)

Located within regulatory regions

Interacting genes (3D)

Treg ChromHMM

FANTOM5 expressed enhancers

chr2

204700689

rs12990970

CTLA4

TssAFlnk

 

CD28,CTLA4,ICOS

204732714

rs231775

TssAFlnk

 

RAPH1,CD28,ICOS

204738919

rs3087243

EnhG

 

RAPH1

chr3

46327588

rs11718385

CCR3

Enh

 

XCR1,CCR2,CCR5AS,CCR5

46391390

rs6441972

CCR2

TssAFlnk

 

CCR3

46401032

rs3138042

Enh

  

46411661

rs2856758

CCR5

Enh

 

SLC6A20,FYCO1,CXCR6,XCR1, LOC105377067,CCR3,CCR1,CCR2

46412259

rs1799988

TssAFlnk

 

SLC6A20, FYCO1,CXCR6, XCR1, LOC105377067,CCR3,CCR1,CCR2

chr5

35852311

rs6890853

IL7R

TssAFlnk

 

SPEF2,LOC105374724,CAPSL

chr6

90948476

rs62408222

BACH2

Enh

 

BACH2,LOC105377891

90983850

rs905671

Enh

✓

BACH2

90984035

rs943689

Enh

✓

BACH2

90995980

rs614120

TssAFlnk

✓

BACH2,LOC105377891

chr7

50462418

rs10216316

IKZF1

EnhG

 

SPATA48

50462498

rs10215297

EnhG

 

SPATA48

50465206

rs55981617

EnhG

 

SPATA48,ZPBP,IKZF1

50465654

rs12670555

EnhG

 

SPATA48,ZPBP,IKZF1,

chr10

6088743

rs12722508

IL2RA

TssAFlnk

 

RMB17

6094697

rs61839660

TssAFlnk

 

IL2RA,RMB17,PFKFB3,LINC02649

6096667

rs12722496

 

✓

IL2RA,RBM17,PFKFB3,LINC02649

6107534

rs11597367

Enh

 

IL2RA,RBM17

chr12

9910720

rs3176793

CD69

TssA

 

LOC374443,CLEC2D

9912182

rs2160086

TssA

 

LOC374443,CLEC2D

9912730

rs3176789

TssA

 

LOC374443,CLEC2D,LOC105369728

9916640

rs3136559

Enh

 

LOC374443,CLEC2D,LOC105369728

9925758

rs1029992

Enh

  

9926064

rs1029991

Enh

  

9926397

rs1029990

Enh

✓

 

9926624

rs10844749

Enh

  

9926784

rs1540356

Enh

  

chr15

38903672

rs16967112

RASGRP1

Enh

✓

FAM98B,RASGRP1,LOC105370775, LOC105370780,LINC02694,FSIP1

38903884

rs56249992

Enh

 

RASGRP1,FAM98B, LOC105370775, LOC105370780,LINC02694,FSIP1

chr16

11188949

rs71136618

CLEC16A

Enh

 

CLEC16A,LOC107984859, LOC105371082,RMI2,SOCS1

chr17

38755665

rs11656173

SMARCE1

Enh

✓

CCR7

chr18

12838767

rs17657058

PTPN2

Enh

 

LINC01882,PTPN2,SEH1L

chr22

30581722

rs5753037

HORMAD2

Enh

 

HORMAD2,LIF-AS1,LIF

  1. The nearest locus indicates the closest gene to the variants in linear distance, while 3D interacting genes are genes in contact with the variants via Treg Hi-C interactions. Overlapped regulatory elements of each 3DFAACTS SNPs are displayed, including chromatin states from a 15-state model and expressed enhancers from FANTOM5. Detailed SNP and interaction information is contained in Additional file 3: Table S3
  2. *Genes in bold indicate novel 3D interacting genes of the identified SNPs