Variant report

Variant	rs6542108
Chromosome Location	chr2:113755190-113755191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113753961..113756170-chr2:113760057..113761673,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1013477	0.85[EUR][1000 genomes]
rs10173618	0.96[ASN][1000 genomes]
rs10196340	0.96[ASN][1000 genomes]
rs10200415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864909	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673918	0.84[EUR][1000 genomes]
rs11686530	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12468503	0.84[EUR][1000 genomes]
rs12711746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711747	0.81[CEU][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13030063	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs13033574	0.85[EUR][1000 genomes]
rs13392494	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13407838	0.96[ASN][1000 genomes]
rs13410389	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1374284	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];0.98[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];1.00[ASN][1000 genomes]
rs1446516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17042691	0.96[ASN][1000 genomes]
rs28938790	0.96[ASN][1000 genomes]
rs28947181	0.83[EUR][1000 genomes]
rs28954071	0.96[ASN][1000 genomes]
rs4849139	0.83[EUR][1000 genomes]
rs4849140	0.86[EUR][1000 genomes]
rs4849142	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs6542109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710007	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs6714534	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6744288	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7571656	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv874878	chr2:113742734-113776076	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113751200-113755600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr2:113751400-113755600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr2:113751800-113755600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:113752000-113755600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr2:113753000-113755200	Enhancers	Dnd41	blood
6	chr2:113753400-113756800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr2:113753600-113755400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:113753600-113755600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:113753600-113755600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:113753800-113755400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:113754400-113755600	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr2:113754600-113755200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr2:113754800-113755400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr2:113754800-113755400	Enhancers	Fetal Lung	lung
15	chr2:113754800-113755600	Enhancers	Fetal Thymus	thymus
16	chr2:113755000-113755600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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