Variant report

Variant	rs7403531
Chromosome Location	chr15:38822905-38822906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11073332	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11073333	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11073334	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593201	0.80[CHB][hapmap];0.84[MEX][hapmap];0.87[AMR][1000 genomes]
rs28582094	0.87[AMR][1000 genomes]
rs72727387	0.80[AMR][1000 genomes]
rs72727388	0.80[AMR][1000 genomes]
rs8043085	0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv904085	chr15:38786114-38985513	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 2 diabetes	22961080	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7403531	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL
rs7403531	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38767800-38827400	Weak transcription	Spleen	Spleen
2	chr15:38768000-38823400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:38795600-38829400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:38804000-38841000	Weak transcription	Dnd41	blood
5	chr15:38804400-38827000	Weak transcription	Esophagus	oesophagus
6	chr15:38807600-38823800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:38812600-38845400	Weak transcription	Fetal Brain Female	brain
8	chr15:38812800-38824400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:38813400-38826400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr15:38814000-38823600	Weak transcription	Brain Anterior Caudate	brain
11	chr15:38814600-38836400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:38815000-38825000	Strong transcription	Thymus	Thymus
13	chr15:38816800-38823800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:38816800-38823800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:38818600-38830200	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr15:38818800-38823000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:38819400-38824400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:38819400-38824400	Enhancers	Osteobl	bone
19	chr15:38820600-38823800	Weak transcription	Primary B cells from cord blood	blood
20	chr15:38820600-38826800	Genic enhancers	Primary T cells from cord blood	blood
21	chr15:38821000-38823600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:38821000-38826200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:38821200-38823600	Weak transcription	NH-A	brain
24	chr15:38821200-38825400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr15:38821200-38825800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:38821400-38823400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:38821400-38824000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:38821400-38830000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr15:38821800-38825000	Strong transcription	Fetal Thymus	thymus
30	chr15:38822000-38829200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr15:38822400-38823200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr15:38822400-38823200	Enhancers	GM12878-XiMat	blood
33	chr15:38822400-38823800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:38822400-38824200	Enhancers	Stomach Mucosa	stomach
35	chr15:38822400-38824600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr15:38822400-38825000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr15:38822600-38823000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:38822600-38823600	Weak transcription	NHDF-Ad	bronchial
39	chr15:38822600-38824000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:38822600-38829400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:38822800-38825200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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