Variant report

Variant	rs2099019
Chromosome Location	chr3:54712786-54712787
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510773	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12488046	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12490327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12490953	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs12496821	1.00[CHB][hapmap]
rs13060843	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13068008	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs13081682	0.89[ASN][1000 genomes]
rs13083683	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs13084602	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13086256	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs13088416	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs13095178	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13096365	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13100029	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1344671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1520575	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17815840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1829549	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1882320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1882322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1921548	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs36061401	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852006	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3864001	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3868872	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3906509	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4083342	1.00[JPT][hapmap]
rs6798481	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs72870697	0.82[ASN][1000 genomes]
rs7618235	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7623961	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7636321	0.89[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54705000-54719000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:54705600-54718800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:54706000-54721600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:54706200-54718400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:54706200-54719400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:54706600-54713000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:54708000-54713200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:54709400-54718600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:54709600-54713400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links