Variant report

Variant	rs703842
Chromosome Location	chr12:58162739-58162740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58162205-58163754	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:58162391-58164419	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:58162468-58164038	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58162243..58164732-chr12:58237977..58240961,2	K562	blood:

Variant related genes	Relation type
METTL21B	TF binding region
ENSG00000257921	TF binding region
CYP27B1	TF binding region
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 41 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1021469	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10431505	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10431552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747786	0.83[JPT][hapmap]
rs10747787	0.83[JPT][hapmap]
rs10783847	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877011	0.85[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10877012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877013	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877014	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877017	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877018	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877029	0.83[JPT][hapmap]
rs10877030	0.83[JPT][hapmap]
rs11172333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172342	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172344	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172349	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172350	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.83[JPT][hapmap]
rs1599931	0.88[JPT][hapmap]
rs1599932	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1875125	0.88[JPT][hapmap]
rs2014886	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2069506	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782130	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4237844	0.83[JPT][hapmap]
rs4646536	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760171	0.83[JPT][hapmap]
rs4760172	0.83[JPT][hapmap]
rs4760332	0.88[JPT][hapmap]
rs4760339	0.82[JPT][hapmap]
rs4760341	0.82[JPT][hapmap]
rs56177740	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581155	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs701008	0.81[TSI][hapmap]
rs724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7965287	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs870392	0.88[JPT][hapmap]
rs871871	0.88[JPT][hapmap]
rs923829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9652011	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
7	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	19525955	GWAS catalog

mRNA abundance (count:40)

SNP	Gene	Cis/trans	Tissue	Source
rs703842	KIAA0748	cis	cerebellum	SCAN
rs703842	FAM119B	cis	cerebellum	SCAN
rs703842	FAM119B	cis	Lymphoblastoid	GTEx
rs703842	ESPL1	cis	parietal	SCAN
rs703842	TSFM	cis	multi-tissue	Pritchard
rs703842	FAM119B	cis	lymphoblastoid	seeQTL
rs703842	FAM119B	cis	Frontal Cortex	GTEx
rs703842	GPR84	cis	cerebellum	SCAN
rs703842	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs703842	CDK4	cis	cerebellum	SCAN
rs703842	FAM119B	cis	parietal	SCAN
rs703842	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs703842	TSFM	cis	Muscle Skeletal	GTEx
rs703842	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs703842	TSPAN31	cis	parietal	SCAN
rs703842	TSPAN31	cis	cerebellum	SCAN
rs703842	XRCC6BP1	cis	Whole Blood	GTEx
rs703842	FAM119B	cis	brain	seeQTL
rs703842	METTL21B	cis	lung	GTEx
rs703842	METTL21B	cis	Esophagus Mucosa	GTEx
rs703842	FAM119B	cis	Cerebellum	GTEx
rs703842	WIBG	cis	cerebellum	SCAN
rs703842	DKFZP586D0919	cis	multi-tissue	Pritchard
rs703842	TSFM	cis	cerebellum	SCAN
rs703842	METTL21B	cis	Adipose Subcutaneous	GTEx
rs703842	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs703842	FAM119B	cis	Temporal Cortex	GTEx
rs703842	TSFM	cis	lymphoblastoid	seeQTL
rs703842	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs703842	KRT5	cis	cerebellum	SCAN
rs703842	METTL21B	cis	Muscle Skeletal	GTEx
rs703842	HSD17B6	cis	cerebellum	SCAN
rs703842	XRCC6BP1	cis	brain	seeQTL
rs703842	METTL21B	cis	Whole Blood	GTEx
rs703842	METTL21B	cis	Nerve Tibial	GTEx
rs703842	METTL21B	cis	Esophagus Muscularis	GTEx
rs703842	TSFM	cis	parietal	SCAN
rs703842	XRCC6BP1	cis	multi-tissue	Pritchard
rs703842	FAM119B	cis	Brain Pons	GTEx
rs703842	FAM119B	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58160800-58163400	Weak transcription	GM12878-XiMat	blood
2	chr12:58160800-58164600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:58160800-58164600	Weak transcription	Right Atrium	heart
4	chr12:58160800-58165200	Weak transcription	Brain Substantia Nigra	brain
5	chr12:58161000-58163000	Weak transcription	Ovary	ovary
6	chr12:58161000-58163000	Weak transcription	Psoas Muscle	Psoas
7	chr12:58161000-58164800	Weak transcription	Right Ventricle	heart
8	chr12:58161000-58165200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:58161000-58165200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:58161000-58165200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:58161200-58164600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:58161200-58164800	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:58161200-58164800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:58161200-58165000	Weak transcription	NH-A	brain
15	chr12:58161200-58165200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:58161400-58162800	Weak transcription	Fetal Lung	lung
17	chr12:58161400-58163000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:58161400-58163000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:58161400-58163800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:58161400-58164600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:58161400-58164600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:58161400-58164800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr12:58161400-58164800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:58161400-58164800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:58161400-58164800	Weak transcription	HUVEC	blood vessel
26	chr12:58161400-58165200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:58161400-58165200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:58161400-58165200	Weak transcription	Colonic Mucosa	Colon
29	chr12:58161600-58163000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:58161600-58163200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:58161600-58164400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr12:58161600-58164600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:58161600-58164600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:58161600-58164800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:58161600-58164800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr12:58161600-58164800	Weak transcription	NHDF-Ad	bronchial
37	chr12:58161800-58162800	Weak transcription	Esophagus	oesophagus
38	chr12:58161800-58163000	Weak transcription	Fetal Brain Female	brain
39	chr12:58161800-58163200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:58161800-58163400	Strong transcription	Pancreas	Pancrea
41	chr12:58161800-58164400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:58161800-58164400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:58161800-58164400	Strong transcription	A549	lung
44	chr12:58161800-58164400	Strong transcription	HSMMtube	muscle
45	chr12:58161800-58164600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:58161800-58164600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:58161800-58164600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:58161800-58164800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:58161800-58164800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:58161800-58164800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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