Variant report

Variant	rs6490279
Chromosome Location	chr12:120436408-120436409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120427086..120431307-chr12:120435070..120439124,5	MCF-7	breast:
2	chr12:120434471..120436415-chr12:120516708..120518666,2	MCF-7	breast:
3	chr12:120425404..120428200-chr12:120435927..120438924,2	K562	blood:

Variant related genes	Relation type
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1054631	0.88[ASN][1000 genomes]
rs16949854	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16949862	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16949870	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16949914	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286041	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28613380	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56105460	0.85[EUR][1000 genomes]
rs56152568	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs56939014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57155388	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57339959	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs57458743	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59868595	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60106911	0.88[ASN][1000 genomes]
rs60223336	0.88[ASN][1000 genomes]
rs60590470	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61514727	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6490282	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7132099	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7139151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7297564	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7298081	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7956221	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7957325	0.90[AFR][1000 genomes];1.00[EUR][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	nsv510575	chr12:120303163-120437490	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1844134	chr12:120426469-120441443	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1845761	chr12:120426469-120441443	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1797666	chr12:120426666-120449259	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv1807589	chr12:120426666-120449259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120428600-120445000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:120428600-120449800	Weak transcription	Brain Anterior Caudate	brain
3	chr12:120428600-120453200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:120428800-120444000	Weak transcription	NHEK	skin
5	chr12:120428800-120444200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:120428800-120447800	Weak transcription	Gastric	stomach
7	chr12:120428800-120451400	Weak transcription	HMEC	breast
8	chr12:120428800-120451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:120429000-120440600	Weak transcription	Fetal Brain Female	brain
10	chr12:120429000-120443800	Weak transcription	Hela-S3	cervix
11	chr12:120429000-120450000	Weak transcription	Esophagus	oesophagus
12	chr12:120429400-120443200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:120429400-120445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:120429800-120445400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:120430000-120437600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:120430400-120439800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:120432600-120441800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:120433000-120444200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:120433200-120437200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:120433200-120441800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr12:120433200-120445000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:120434200-120444800	Weak transcription	Primary B cells from cord blood	blood
23	chr12:120434400-120437600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:120434600-120436600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:120435200-120439000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:120435200-120441800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:120435600-120436800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:120435600-120436800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:120435800-120437000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:120436200-120436600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:120436200-120436600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:120436200-120436800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:120436200-120437000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:120436200-120438000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:120436200-120438600	Strong transcription	Thymus	Thymus
36	chr12:120436200-120440400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:120436200-120440400	Strong transcription	Fetal Thymus	thymus
38	chr12:120436200-120442000	Strong transcription	Primary T cells from cord blood	blood
39	chr12:120436400-120436600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:120436400-120437000	Enhancers	Fetal Intestine Large	intestine
41	chr12:120436400-120438000	Weak transcription	Fetal Intestine Small	intestine
42	chr12:120436400-120441600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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