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Table 3 Genes assigned to T and/or B cells based on posterior probability of SNPs in enhancers

From: Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability

Locus

Chr

SNP cate gory

FLS, T, B, ALL, NONE (based on posteriors of SNPs in enhancers)

Top posterior rs numbers

Jurkat T cells proximal genes

Jurkat T cells distal genes

GM12878 B cells proximal genes

GM12878 B cells distal genes

5

chr1

1

B CELL

rs6679677, rs2476601

RSBN1; PHTF1; PTPN22

RSBN1; PHTF1; PTPN22; AP4B1; HIPK1-AS1; HIPK1; OLFML3

RSBN1; PHTF1; PTPN22

RSBN1; PTPN22; PHTF1; AP4B1-AS1; BCL2L15; AP4B1; HIPK1-AS1; HIPK1; OLFML3; LRIG2

6

chr1

2

B CELL

rs1217404, rs2476604, rs1217420

RSBN1; PHTF1; PTPN22; AP4B1-AS1

RSBN1; PHTF1; PTPN22; AP4B1; HIPK1-AS1; HIPK1; OLFML3

RSBN1; PHTF1; PTPN22; AP4B1-AS1

PTPN22; RSBN1; PHTF1; AP4B1-AS1; BCL2L15; AP4B1; HIPK1-AS1; HIPK1; OLFML3; LRIG2; FRMD8; ARL13B; STX19

8

1

3

B CELL

rs4657041, rs1801274, rs6671847

FCGR2A

FCER1G; NDUFS2; SDHC; MPZ; CFAP126; FCGR2A; FCGR2B; FCRLA; FCRLB; RN7SL466P; DUSP12; ATF6; PCP4L1; ADAMTS4

FCGR2A

SDHC; MPZ; FCGR2A; FCGR2B; FCRLA; FCRLB; RN7SL466P; DUSP12; ATF6; CFAP126; RNU6- 481P; ADAMTS4; NDUFS2

10

chr2

1

ALL

rs10175798, rs10173253, rs906868, rs7579944

LBH

LBH

LBH

LBH; LCLAT1

11

chr2

2

ALL

rs34695944, rs56095903, rs67574266, rs13031237, rs13031721

LINC01185; REL; RNU4- 51P

LINC01185; REL; RNU4- 51P; PUS10; PAPOLG; RN7SL632P; RNA5SP95; B3GNT2; RNU6-612P

LINC01185; REL; RNU4- 51P

LINC01185; REL; RNU4- 51P; PUS10; PAPOLG; RN7SL632P; RNA5SP95; B3GNT2; RNU6-612P

14

chr2

3

T CELL

rs13426947, rs3024859, rs7568275, rs11889341

STAT4

STAT4; RNU6-959P; MYO1B

STAT4

STAT4; RNU6-959P

16

chr2

3

T CELL

rs1980421, rs1980422, rs7588874, rs7422494

CD28; RNU6-474P;

CTLA4

CD28; RNU6-474P; CTLA4; RAPH1; ABI2

CD28; RNU6-474P; CTLA4

CD28; CTLA4; RNU6-474P; RAPH1; PRKG1

17

chr2

1

T CELL

rs231724, rs231723, rs231775

CTLA4

CTLA4; CD28; RNU6- 474P; RAPH1

CTLA4

CD28; CTLA4; RNU6- 474P; RAPH1

19

 

2

T CELL, B CELL

rs9310852, rs4680838, rs9880772, rs1353286

EOMES

LINC02084; EOMES; LINC01967; CMC1; AZI2; ZCWPW2; NEK10;

LINC01980

EOMES

LINC02084; EOMES; CMC1; AZI2; ZCWPW2

20

chr3

1

ALL

rs73081554, rs185407974, rs180977001, rs35677470, rs114584537

FLNB; DNASE1L3; FLNB- AS1; ABHD6; RPP14; HTD2; PXK

DNASE1L3; ABHD6; RPP14; HTD2; PXK; PDHB; KCTD6; ACOX2; FAM107A; FAM3D-AS1; FAM3D; FLNB

FLNB; DNASE1L3; FLNB- AS1; ABHD6; RPP14; HTD2; PXK

DNASE1L3; ABHD6; RPP14; HTD2; PXK; FLNB; FLNB-AS1; PDHB; KCTD6; ACOX2; FAM107A; FAM3D-AS1; FAM3D

24

chr5

1

T CELL

rs7731626

ANKRD55

ANKRD55; RNA5SP184; IL6ST

ANKRD55

ANKRD55; RNU6-299P; RNA5SP184; IL31RA; IL6ST

28

chr6

3

ALL

 

TMEM151B; AARS2; NFKBIE; TCTE1

TMEM151B; AARS2; TCTE1; HSP90AB1; SLC35B2; MIR4647; NFKBIE; SPATS1; CAPN11; TMEM63B; RN7SL811P

TMEM151B; AARS2; NFKBIE; TCTE1

TMEM151B; AARS2; TCTE1; NFKBIE; HSP90AB1; SLC35B2; MIR4647; MRPL14; TMEM63B; SPATS1; TRIM38; CAPN11; MTX2

31

chr6

2

B CELL

rs2451258, rs2485363, rs654690 , rs1994564, rs212389

 

RSPH3; TAGAP; SYTL3;

C6orf99

 

RSPH3; TAGAP; SYTL3; C11orf44

32

chr6

1

T CELL, B CELL

rs1571878, rs3093017, rs10946216

CCR6

CCR6; RPS6KA2

CCR6

CCR6; SFT2D1; RPS6KA2; RNASET2; MIR3939; FGFR1OP; GPR31; PPIL4

33

chr7

2

ALL

rs186735625, rs57585717, rs2158624

JAZF1; JAZF1-AS1; RNU6- 979P

JAZF1; RNU6-979P; JAZF1-AS1; HOTTIP; HOXA1; HOTAIRM1; HOXA3; HOXA-AS2; HOXA4; HOXA5; HOXA6; HOXA-AS3; HOXA7; HOXA9; HOXA10-AS; MIR196B; HOXA10; HOXA11; HOXA11-AS; EVX1-AS; EVX1

JAZF1; JAZF1-AS1; RNU6- 979P

JAZF1; RNU6-979P; JAZF1-AS1; HOTTIP; HOXA11; HOXA11-AS; HOXA1; HOTAIRM1; HOXA3; HOXA-AS2; HOXA4; HOXA5; HOXA- AS3; HOXA7; HOXA9; HOXA10-AS; MIR196B; HOXA10; EVX1-AS; EVX1; HOXA6; PARP9

34

chr7

3

FLS, B CELL

rs4272, rs8179, rs42034

CDK6

CDK6; PEX1; RBM48; FAM133B; CDK6-AS1; SAMD9; VPS50; HEPACAM2

CDK6

CDK6; FAM133B; SAMD9; CDK6-AS1