Variant report

Variant	rs4680353
Chromosome Location	chr3:157004323-157004324
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1014855	0.85[JPT][hapmap]
rs10513510	0.82[CHB][hapmap]
rs10513512	0.81[CHB][hapmap]
rs1074864	0.85[JPT][hapmap]
rs10755111	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10804777	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10936063	0.82[CHB][hapmap]
rs10936066	0.82[CHB][hapmap]
rs10936075	0.84[ASN][1000 genomes]
rs10936077	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10936088	0.85[JPT][hapmap]
rs10936089	0.85[JPT][hapmap]
rs12486155	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12486304	0.81[AMR][1000 genomes]
rs12486955	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12490120	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12492801	0.82[CHB][hapmap]
rs12494423	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs12496111	0.81[CHB][hapmap]
rs12632562	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12633099	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12633429	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12634905	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12636125	0.82[CHB][hapmap]
rs12637932	0.85[CEU][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1403105	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1403106	0.91[CHB][hapmap]
rs1403108	0.86[CHB][hapmap]
rs1403109	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1456104	0.85[JPT][hapmap]
rs1456109	0.85[JPT][hapmap]
rs1500923	0.83[TSI][hapmap]
rs1522393	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1546260	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1568611	0.86[CHB][hapmap]
rs1581413	0.83[TSI][hapmap]
rs1995304	0.82[CHB][hapmap]
rs2047647	0.85[CEU][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2321743	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2874616	0.91[CHB][hapmap]
rs4679789	0.85[ASN][1000 genomes]
rs4679790	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679791	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680340	0.82[CHB][hapmap]
rs4680343	0.82[CHB][hapmap]
rs4680345	0.81[CHB][hapmap]
rs4680352	0.91[CHB][hapmap]
rs5003893	0.82[CHB][hapmap]
rs55734537	0.90[AMR][1000 genomes]
rs56150358	0.81[ASN][1000 genomes]
rs6441115	0.82[CHB][hapmap]
rs6441116	0.82[CHB][hapmap]
rs6781682	0.82[CHB][hapmap]
rs6805989	0.82[CHB][hapmap]
rs6809307	0.82[CHB][hapmap]
rs73156724	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7621912	0.82[CHB][hapmap]
rs7648599	0.82[CHB][hapmap]
rs7649737	0.86[CHB][hapmap]
rs7652298	0.91[CHB][hapmap]
rs872652	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8925	0.81[CHB][hapmap]
rs9831686	0.85[JPT][hapmap]
rs9848774	0.85[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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4680353	SSR3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156967200-157007800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:156988000-157005800	Weak transcription	Pancreas	Pancrea
3	chr3:156997000-157004400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:156998800-157006000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:157000600-157015400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:157001600-157008200	Weak transcription	NH-A	brain
7	chr3:157001800-157004400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:157003000-157004400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:157003000-157004600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:157003200-157004600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:157003400-157004400	Genic enhancers	Osteobl	bone
12	chr3:157003600-157004600	Weak transcription	Fetal Brain Female	brain
13	chr3:157003600-157007400	Weak transcription	Fetal Stomach	stomach
14	chr3:157003600-157011800	Weak transcription	Fetal Lung	lung
15	chr3:157003800-157004800	Enhancers	HUVEC	blood vessel
16	chr3:157003800-157007600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:157004000-157004400	Genic enhancers	NHDF-Ad	bronchial
18	chr3:157004000-157005600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:157004000-157007000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:157004200-157004400	Enhancers	Spleen	Spleen
21	chr3:157004200-157004600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:157004200-157007400	Weak transcription	NHLF	lung

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