Variant report

Variant	rs3805962
Chromosome Location	chr6:70648790-70648791
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:70646120..70647757-chr6:70648588..70650873,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082293	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10485244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17766479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096058	0.88[ASN][1000 genomes]
rs2345744	0.89[CEU][hapmap]
rs3793031	0.82[EUR][1000 genomes]
rs3793032	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3793033	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3793035	1.00[CEU][hapmap]
rs3793036	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3793038	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3805961	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805971	1.00[AMR][1000 genomes]
rs3805973	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805978	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs3805986	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3805987	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs56293172	0.82[EUR][1000 genomes]
rs56922945	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59501442	0.82[EUR][1000 genomes]
rs59599861	0.82[EUR][1000 genomes]
rs59707679	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60134810	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903421	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6935032	0.81[CHB][hapmap]
rs6935585	0.91[CEU][hapmap]
rs6938320	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742627	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7756062	0.91[CEU][hapmap]
rs7761968	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9446170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9446172	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9446178	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9454908	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9454910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9454914	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9454930	0.90[CEU][hapmap]
rs9454935	0.91[CEU][hapmap]
rs978291	0.88[CHB][hapmap];0.89[JPT][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	nsv886140	chr6:70354682-70728202	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv886141	chr6:70590638-70694162	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1026151	chr6:70621616-70946967	Enhancers Weak transcription Flanking Active TSS Active TSS 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	5 gene(s)	inside rSNPs	diseases
4	nsv463151	chr6:70625166-70694162	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv603636	chr6:70625166-70694162	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 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	chr6:70642200-70653800	Strong transcription	Primary B cells from peripheral blood	blood
2	chr6:70642800-70649800	Strong transcription	Primary B cells from cord blood	blood
3	chr6:70647600-70648800	Enhancers	Fetal Heart	heart
4	chr6:70648200-70649600	Active TSS	Right Atrium	heart
5	chr6:70648400-70648800	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links