Variant report

Variant	rs2359790
Chromosome Location	chr3:54387169-54387170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12632768	0.80[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs13327625	0.96[EUR][1000 genomes]
rs1449326	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs1449327	0.84[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1449328	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1449329	0.86[CEU][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1449330	0.81[CEU][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1473345	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1473346	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1473347	0.85[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1473348	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs1868497	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1868502	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1868506	0.87[EUR][1000 genomes]
rs1868507	0.87[EUR][1000 genomes]
rs1868508	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs1975611	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1992963	0.85[GIH][hapmap]
rs1992964	0.91[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs2359789	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2359792	0.95[EUR][1000 genomes]
rs2359793	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4025912	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs4131315	0.85[GIH][hapmap];0.83[JPT][hapmap]
rs4974369	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs4974370	0.80[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs6768189	0.93[CHB][hapmap]
rs731507	0.83[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7372444	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7372695	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7428295	0.93[CHB][hapmap]
rs7429237	0.85[GIH][hapmap];0.83[JPT][hapmap]
rs7431094	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7648293	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs7653648	0.82[TSI][hapmap]
rs9827201	1.00[CEU][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes]
rs9830682	0.86[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9836159	0.85[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9841318	0.83[JPT][hapmap]
rs9851130	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs9862712	0.86[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9862718	0.86[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9870407	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9877288	0.86[EUR][1000 genomes]
rs9877455	0.94[EUR][1000 genomes]
rs9877529	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs9882299	0.92[CHB][hapmap];0.86[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2359790	SEMA3G	cis	parietal	SCAN
rs2359790	TKT	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54378800-54389000	Weak transcription	Psoas Muscle	Psoas
2	chr3:54380000-54391200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:54380200-54387200	Weak transcription	Ovary	ovary
4	chr3:54382800-54387200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:54383400-54387400	Weak transcription	Left Ventricle	heart
6	chr3:54383400-54387600	Weak transcription	Right Atrium	heart
7	chr3:54383400-54392600	Weak transcription	Right Ventricle	heart
8	chr3:54384000-54392400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:54384200-54387600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:54384800-54387200	Weak transcription	Fetal Lung	lung
11	chr3:54385800-54387600	Enhancers	Hela-S3	cervix
12	chr3:54386000-54387800	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links