Variant report

Variant	rs1132838
Chromosome Location	chr2:10053610-10053611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10047372..10050689-chr2:10052531..10055799,4	MCF-7	breast:
2	chr2:10053405..10055914-chr2:10061703..10064557,2	K562	blood:
3	chr2:10053405..10055914-chr2:10061703..10065567,3	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1014509	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1036056	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1036057	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1036058	0.97[ASN][1000 genomes]
rs10495575	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1062160	0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10929617	0.95[ASN][1000 genomes]
rs10929618	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12468582	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12470216	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12476490	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12478489	0.89[ASN][1000 genomes]
rs12611655	0.95[ASN][1000 genomes]
rs12613533	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12613568	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12617615	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12619769	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12621415	0.91[ASN][1000 genomes]
rs12622420	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12623017	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12623213	0.88[ASN][1000 genomes]
rs12623372	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1367386	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1469542	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469543	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1469544	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469545	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1469546	0.89[ASN][1000 genomes]
rs1473962	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs16867195	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs16867196	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs16867211	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs16867215	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16867242	1.00[ASN][1000 genomes]
rs1835427	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967517	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1967518	0.90[ASN][1000 genomes]
rs2280150	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280151	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288640	0.86[ASN][1000 genomes]
rs2288644	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4143791	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4143792	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4143793	0.88[ASN][1000 genomes]
rs4444493	1.00[LWK][hapmap]
rs452480	0.87[ASN][1000 genomes]
rs4610025	0.93[ASN][1000 genomes]
rs4627538	0.86[ASN][1000 genomes]
rs4669470	1.00[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4669471	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4669472	0.91[ASN][1000 genomes]
rs4669473	0.91[ASN][1000 genomes]
rs4669475	0.93[ASN][1000 genomes]
rs4669476	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4669477	0.95[ASN][1000 genomes]
rs4669478	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4669479	0.96[ASN][1000 genomes]
rs4669481	0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4669484	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4669485	0.99[ASN][1000 genomes]
rs4669486	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669501	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4669506	0.87[ASN][1000 genomes]
rs59288259	0.90[ASN][1000 genomes]
rs62127130	0.93[ASN][1000 genomes]
rs62127133	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62127134	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62127136	0.93[ASN][1000 genomes]
rs62127137	0.92[ASN][1000 genomes]
rs62127138	0.95[ASN][1000 genomes]
rs62127140	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62127143	0.96[ASN][1000 genomes]
rs62127144	0.96[ASN][1000 genomes]
rs62127145	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127146	0.98[ASN][1000 genomes]
rs62127463	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62127466	0.98[ASN][1000 genomes]
rs62127471	0.89[ASN][1000 genomes]
rs62127563	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62127564	0.91[ASN][1000 genomes]
rs62127565	0.91[ASN][1000 genomes]
rs62129896	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707551	0.91[ASN][1000 genomes]
rs718255	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs718256	0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs72782621	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72782635	0.95[ASN][1000 genomes]
rs7563385	0.90[ASN][1000 genomes]
rs7579559	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7602449	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7608055	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv1006533	chr2:10030964-10065624	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1004743	chr2:10031389-10065624	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1005938	chr2:10043181-10074384	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1003855	chr2:10045055-10059844	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1132838	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs1132838	TAF1B	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:9999200-10053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
4	chr2:10024400-10053800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr2:10025000-10053800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:10025000-10053800	Weak transcription	Ovary	ovary
7	chr2:10025000-10054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:10025000-10054400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:10025000-10054400	Weak transcription	Spleen	Spleen
10	chr2:10026000-10072800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:10028200-10053800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
13	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:10036000-10065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:10036800-10073000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:10037800-10075600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:10038000-10053800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:10038400-10053800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:10038400-10053800	Weak transcription	GM12878-XiMat	blood
22	chr2:10038400-10054400	Weak transcription	NHLF	lung
23	chr2:10038400-10054600	Weak transcription	Fetal Brain Female	brain
24	chr2:10038600-10054400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:10038600-10054400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:10038600-10054400	Weak transcription	Small Intestine	intestine
27	chr2:10038600-10054400	Weak transcription	Hela-S3	cervix
28	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:10038800-10054400	Weak transcription	NHEK	skin
31	chr2:10039000-10058600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:10039400-10059400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:10042600-10077000	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:10044200-10065200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:10045000-10056600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:10045000-10058400	Weak transcription	Psoas Muscle	Psoas
37	chr2:10045600-10054400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
39	chr2:10046000-10075200	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:10047200-10056800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:10047200-10061600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
43	chr2:10047800-10054400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:10047800-10054400	Weak transcription	Fetal Stomach	stomach
45	chr2:10048000-10053800	Weak transcription	Fetal Intestine Large	intestine
46	chr2:10048200-10053800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:10048200-10053800	Weak transcription	Thymus	Thymus
48	chr2:10048600-10058400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:10049000-10054400	Weak transcription	Lung	lung
50	chr2:10049000-10077400	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links