Variant report

Variant	rs1500923
Chromosome Location	chr3:157049324-157049325
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10755111	0.83[TSI][hapmap]
rs10936077	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10936079	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12486155	0.81[EUR][1000 genomes]
rs12486955	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12494423	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12636252	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1392798	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1403105	0.83[TSI][hapmap]
rs1500921	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1522393	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1546260	0.83[TSI][hapmap]
rs1566521	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1581413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2321743	0.83[TSI][hapmap]
rs34263112	0.82[ASN][1000 genomes]
rs4680353	0.83[TSI][hapmap]
rs55734537	0.82[EUR][1000 genomes]
rs56311637	0.90[ASN][1000 genomes]
rs62278578	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62278580	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62281378	0.91[EUR][1000 genomes]
rs73156724	0.80[EUR][1000 genomes]
rs73156728	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7642909	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs991083	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv275099	chr3:157046192-157049852	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1500923	SSR3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157036800-157053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:157039800-157051000	Weak transcription	HUVEC	blood vessel
3	chr3:157041000-157065600	Weak transcription	Pancreas	Pancrea
4	chr3:157046600-157049400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:157047200-157049600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:157047400-157050000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:157047600-157049800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:157047800-157051200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:157048000-157051000	Weak transcription	NHLF	lung
10	chr3:157048000-157054600	Enhancers	NHDF-Ad	bronchial
11	chr3:157048200-157051000	Weak transcription	Osteobl	bone
12	chr3:157048200-157057000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:157048400-157049400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:157048400-157051000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:157049000-157050400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:157049200-157050600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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