Variant report

Variant	rs12208927
Chromosome Location	chr6:143993634-143993635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143993420..143996184-chr6:143997864..144000506,3	MCF-7	breast:
2	chr6:143993282..143995063-chr6:144073784..144075986,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10872562	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108314	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.90[ASN][1000 genomes]
rs11155315	0.86[CHB][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs11155317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12198291	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12206069	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12207002	1.00[ASW][hapmap];0.85[CEU][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];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3924969	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3934959	0.82[ASN][1000 genomes]
rs6901659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6907410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913134	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.87[ASN][1000 genomes]
rs6915784	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6931801	0.86[GIH][hapmap]
rs7740709	0.84[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs7741424	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748882	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs7766510	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7769294	0.82[ASN][1000 genomes]
rs7772565	0.86[CHB][hapmap];0.80[CHD][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs7776119	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8180640	0.89[ASN][1000 genomes]
rs9373396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9373397	0.94[JPT][hapmap]
rs9376776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376779	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9386042	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs9386043	0.94[JPT][hapmap]
rs9390126	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399458	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403521	1.00[ASW][hapmap];1.00[CEU][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[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403523	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9496739	0.86[CHD][hapmap]

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	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143980800-143994200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:143981800-143994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:143991400-143994200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:143992600-143994000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:143993400-143995600	Weak transcription	Aorta	Aorta
6	chr6:143993600-143994200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:143993600-143994400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:143993600-143994600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr6:143993600-143996400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:143993600-143996800	Enhancers	Placenta	Placenta

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