Variant report

Variant	rs10245053
Chromosome Location	chr7:38532366-38532367
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10085389	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs1019286	0.82[JPT][hapmap]
rs1019287	0.82[JPT][hapmap]
rs10229905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230064	0.84[CEU][hapmap]
rs10232299	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10238666	0.85[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246472	0.82[JPT][hapmap]
rs10247761	0.85[ASN][1000 genomes]
rs10248732	0.82[JPT][hapmap]
rs10249106	0.82[JPT][hapmap]
rs10249698	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250232	0.86[CEU][hapmap]
rs10250342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10255786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259475	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264790	0.82[JPT][hapmap]
rs10264958	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10276324	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10276544	0.82[JPT][hapmap]
rs10277878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280133	1.00[JPT][hapmap]
rs10280220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281867	0.82[CEU][hapmap]
rs1030016	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs11486852	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158376	0.85[ASN][1000 genomes]
rs11763753	0.82[CHB][hapmap]
rs2014872	0.96[ASN][1000 genomes]
rs2267807	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2267811	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28412720	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2893559	0.85[ASN][1000 genomes]
rs3807390	1.00[JPT][hapmap]
rs3823595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4419725	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723756	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57983498	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120255	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7799083	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10245053	GPR141	cis	parietal	SCAN
rs10245053	TBX20	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38502600-38549400	Weak transcription	Fetal Stomach	stomach
2	chr7:38502800-38533800	Weak transcription	Aorta	Aorta
3	chr7:38524000-38543400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:38524200-38545000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:38528600-38553000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:38531400-38544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:38531800-38543800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:38532000-38540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links