Variant report

Variant	rs12541410
Chromosome Location	chr8:99355612-99355613
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	chr8:99354049..99356109-chr8:99374598..99376859,2	MCF-7	breast:
2	chr8:99302112..99311881-chr8:99336694..99356691,43	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104361	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10955163	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10955164	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11990127	0.90[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12375289	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12542247	0.91[ASN][1000 genomes]
rs12545666	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12546215	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12547347	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13259687	0.82[YRI][hapmap]
rs13278348	0.90[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16892233	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16896889	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34468294	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35717300	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35841793	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4346964	0.82[YRI][hapmap]
rs4463387	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4543515	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6996904	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6997055	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7002877	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7008701	0.80[CEU][hapmap]
rs71514986	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71514987	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73285674	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7820378	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7837340	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7842811	0.80[CEU][hapmap]
rs7843256	0.80[CEU][hapmap]
rs9642950	0.90[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv831406	chr8:99290745-99482076	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv891217	chr8:99346537-99391285	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99352400-99355800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr8:99354200-99368200	Weak transcription	NHDF-Ad	bronchial
3	chr8:99354600-99369000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:99355200-99356000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr8:99355200-99356400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:99355400-99355800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:99355400-99356000	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links