Variant report

Variant	rs9855860
Chromosome Location	chr3:54466342-54466343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12493552	0.94[CEU][hapmap]
rs12632768	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs13327362	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1449326	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1449327	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1449328	0.86[ASN][1000 genomes]
rs1449329	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1449330	1.00[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs1449333	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1473345	0.86[ASN][1000 genomes]
rs1473346	0.86[ASN][1000 genomes]
rs1473347	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1530732	0.87[CEU][hapmap]
rs1868497	0.86[ASN][1000 genomes]
rs1868500	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1868502	0.89[ASN][1000 genomes]
rs1975611	0.87[ASN][1000 genomes]
rs1992963	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs1992964	0.86[JPT][hapmap]
rs2359789	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs4131315	0.80[JPT][hapmap]
rs4974360	0.87[CEU][hapmap]
rs4974361	0.88[CEU][hapmap]
rs4974368	0.88[CEU][hapmap]
rs4974369	0.94[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4974370	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6445664	0.94[CEU][hapmap]
rs6768189	0.86[JPT][hapmap]
rs73089428	0.83[EUR][1000 genomes]
rs73089448	0.81[EUR][1000 genomes]
rs73089451	0.81[EUR][1000 genomes]
rs731507	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7372444	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs7372695	0.89[ASN][1000 genomes]
rs7428295	0.86[JPT][hapmap]
rs7429237	0.80[JPT][hapmap]
rs7615599	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7624727	0.94[CEU][hapmap]
rs7648293	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7652529	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9311528	1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs9311529	0.86[JPT][hapmap]
rs9827201	0.86[CHB][hapmap]
rs9830682	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs9836159	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs9841318	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs9841979	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9851130	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs9861155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862712	1.00[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs9862718	1.00[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs9870407	1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs9877529	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs9882299	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	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
4	nsv1010348	chr3:54435563-54508115	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv876807	chr3:54453655-54501086	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv998970	chr3:54455794-54516789	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv876808	chr3:54459688-54501086	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv876809	chr3:54459688-54501086	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54462200-54467600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:54462800-54467600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:54463000-54466600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:54463000-54469200	Weak transcription	Hela-S3	cervix
5	chr3:54463400-54467600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:54463600-54469000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:54463600-54469000	Weak transcription	NHDF-Ad	bronchial

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