Variant report

Variant	rs9379988
Chromosome Location	chr6:27524272-27524273
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27524150..27526168-chr6:27529361..27532636,4	MCF-7	breast:
2	chr6:27522451..27525164-chr6:27546667..27548456,2	K562	blood:
3	chr6:27522886..27525493-chr6:27528016..27530032,2	K562	blood:
4	chr6:27524177..27527153-chr6:27531672..27535728,3	MCF-7	breast:
5	chr6:27516900..27519076-chr6:27523913..27526457,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000219738	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1010261	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs12174918	0.88[AMR][1000 genomes]
rs13201294	0.90[ASN][1000 genomes]
rs16867962	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs2394001	0.88[AMR][1000 genomes]
rs4711158	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711161	1.00[AMR][1000 genomes]
rs4713116	0.83[AMR][1000 genomes]
rs4713117	0.91[AMR][1000 genomes]
rs4713122	0.88[AMR][1000 genomes]
rs56911191	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58727692	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59015666	0.88[AMR][1000 genomes]
rs9357041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9368515	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9368516	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[AMR][1000 genomes]
rs9379987	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9379989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379991	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9379993	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9379997	0.83[AMR][1000 genomes]
rs9380009	0.88[AMR][1000 genomes]
rs9380013	0.88[AMR][1000 genomes]
rs9380014	0.91[AMR][1000 genomes]
rs9380015	0.88[AMR][1000 genomes]
rs9393825	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9393829	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9393845	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[AMR][1000 genomes]
rs9393854	1.00[CEU][hapmap]
rs9393855	0.91[AMR][1000 genomes]
rs9468183	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27522400-27526000	Weak transcription	K562	blood
2	chr6:27523600-27525000	Bivalent Enhancer	Placenta	Placenta
3	chr6:27523800-27524600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27523800-27524800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:27524000-27524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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