Variant report

Variant	rs4646536
Chromosome Location	chr12:58157988-58157989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58155623..58158327-chr12:58204942..58207144,2	MCF-7	breast:
2	chr12:58156406..58160029-chr12:58238044..58241191,3	MCF-7	breast:
3	chr12:58156984..58159427-chr17:57858863..57860649,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 32 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1021469	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10431505	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10431552	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];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747786	0.83[JPT][hapmap]
rs10747787	0.83[JPT][hapmap]
rs10783847	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877013	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877017	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877018	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877029	0.83[JPT][hapmap]
rs10877030	0.83[JPT][hapmap]
rs11172333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172342	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172344	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172349	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172350	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.83[JPT][hapmap]
rs1599931	0.88[JPT][hapmap]
rs1599932	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1875124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875125	0.88[JPT][hapmap]
rs2014886	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2069502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069506	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782130	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4237844	0.83[JPT][hapmap]
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	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6581155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs701008	0.81[TSI][hapmap]
rs703842	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]
rs724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7489290	0.81[YRI][hapmap]
rs7965287	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8181644	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];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9652011	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs4646536	METTL21B	cis	Adipose Subcutaneous	GTEx
rs4646536	TSPAN31	cis	parietal	SCAN
rs4646536	XRCC6BP1	cis	multi-tissue	Pritchard
rs4646536	FAM119B	cis	parietal	SCAN
rs4646536	DKFZP586D0919	cis	multi-tissue	Pritchard
rs4646536	METTL21B	cis	Esophagus Muscularis	GTEx
rs4646536	GPR84	cis	cerebellum	SCAN
rs4646536	METTL21B	cis	lung	GTEx
rs4646536	KRT5	cis	cerebellum	SCAN
rs4646536	TSPAN31	cis	cerebellum	SCAN
rs4646536	KIAA0748	cis	cerebellum	SCAN
rs4646536	XRCC6BP1	cis	Whole Blood	GTEx
rs4646536	ESPL1	cis	parietal	SCAN
rs4646536	METTL21B	cis	Muscle Skeletal	GTEx
rs4646536	METTL21B	cis	Whole Blood	GTEx
rs4646536	FAM119B	cis	cerebellum	SCAN
rs4646536	HSD17B6	cis	cerebellum	SCAN
rs4646536	CDK4	cis	cerebellum	SCAN
rs4646536	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs4646536	TSFM	cis	cerebellum	SCAN
rs4646536	METTL21B	cis	Esophagus Mucosa	GTEx
rs4646536	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs4646536	TSFM	cis	parietal	SCAN
rs4646536	WIBG	cis	cerebellum	SCAN
rs4646536	TSFM	cis	multi-tissue	Pritchard
rs4646536	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4646536	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs4646536	TSFM	cis	Muscle Skeletal	GTEx
rs4646536	FAM119B	cis	lymphoblastoid	seeQTL
rs4646536	TSFM	cis	lymphoblastoid	seeQTL
rs4646536	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs4646536	METTL21B	cis	Heart Left Ventricle	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58150400-58158400	Weak transcription	Right Atrium	heart
2	chr12:58150600-58158600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:58152200-58160000	Weak transcription	K562	blood
4	chr12:58152800-58158000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:58153000-58158000	Weak transcription	GM12878-XiMat	blood
6	chr12:58153000-58158200	Weak transcription	Gastric	stomach
7	chr12:58153200-58158000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:58153200-58158000	Weak transcription	Esophagus	oesophagus
9	chr12:58153200-58158000	Weak transcription	Lung	lung
10	chr12:58153400-58158000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:58153400-58158000	Weak transcription	Placenta	Placenta
12	chr12:58153600-58158200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:58153800-58158200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:58154000-58158200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:58154000-58158200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:58154000-58158200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:58154000-58162200	Weak transcription	Dnd41	blood
18	chr12:58154800-58160000	Weak transcription	Aorta	Aorta
19	chr12:58155000-58158000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:58155800-58158400	Weak transcription	HepG2	liver
21	chr12:58156600-58158000	Genic enhancers	HMEC	breast
22	chr12:58156600-58159000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:58156600-58159000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:58156600-58159000	Transcr. at gene 5' and 3'	NHEK	skin
25	chr12:58156800-58161400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:58157000-58158000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:58157000-58162200	Weak transcription	Hela-S3	cervix
28	chr12:58157400-58158000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
29	chr12:58157400-58158000	Enhancers	Pancreas	Pancrea
30	chr12:58157400-58158200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:58157400-58158400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr12:58157400-58158600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:58157400-58159200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:58157800-58158000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
35	chr12:58157800-58158000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
36	chr12:58157800-58158200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:58157800-58158400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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