Variant report

Variant	rs1992964
Chromosome Location	chr3:54463125-54463126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12493552	0.82[CHB][hapmap]
rs12632768	0.93[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs13082754	0.82[CEU][hapmap]
rs1375521	0.81[CEU][hapmap]
rs1449326	0.81[JPT][hapmap]
rs1449327	0.84[JPT][hapmap]
rs1449329	0.81[JPT][hapmap]
rs1449330	0.81[JPT][hapmap]
rs1449333	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs1473345	0.83[EUR][1000 genomes]
rs1473346	0.83[EUR][1000 genomes]
rs1473347	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1473348	0.88[GIH][hapmap]
rs1530732	0.82[CHB][hapmap]
rs1868502	0.84[EUR][1000 genomes]
rs1868508	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1975611	0.83[EUR][1000 genomes]
rs1992963	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2359789	0.81[CEU][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs2359790	0.91[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs2359793	0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap]
rs4025912	0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap]
rs4131315	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4974370	0.93[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs6445655	0.81[CEU][hapmap]
rs6445657	0.82[EUR][1000 genomes]
rs6445660	0.93[ASN][1000 genomes]
rs6445664	0.82[CHB][hapmap]
rs6768189	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs6777368	0.82[EUR][1000 genomes]
rs6804196	0.82[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap]
rs73089420	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731507	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs731508	0.82[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs7426795	0.83[CEU][hapmap]
rs7428295	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs7429237	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7615599	0.82[CHB][hapmap]
rs7624727	0.82[CHB][hapmap]
rs7648293	0.87[JPT][hapmap]
rs7652529	0.96[ASN][1000 genomes]
rs7653648	0.82[GIH][hapmap]
rs9817603	0.82[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap]
rs9827201	0.87[JPT][hapmap]
rs9830682	0.81[JPT][hapmap]
rs9836159	0.81[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs9841318	0.81[JPT][hapmap]
rs9843412	0.82[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap]
rs9851130	0.81[JPT][hapmap]
rs9855860	0.86[JPT][hapmap]
rs9861155	0.93[JPT][hapmap]
rs9862712	0.83[ASW][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap]
rs9862718	0.83[ASW][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap]
rs9870407	0.81[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9877529	0.81[JPT][hapmap]
rs9882285	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882553	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54460600-54463600	Enhancers	NHDF-Ad	bronchial
2	chr3:54461000-54463200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:54461200-54463200	Enhancers	Fetal Muscle Leg	muscle
4	chr3:54461600-54463400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:54461600-54463400	Enhancers	Fetal Brain Male	brain
6	chr3:54462200-54467600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:54462400-54463200	Enhancers	NH-A	brain
8	chr3:54462600-54463600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:54462800-54463200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:54462800-54463200	Enhancers	Brain Germinal Matrix	brain
11	chr3:54462800-54467600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:54463000-54463200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:54463000-54463600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:54463000-54466600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:54463000-54469200	Weak transcription	Hela-S3	cervix

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