Variant report

Variant	rs939115
Chromosome Location	chr3:158239323-158239324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10513526	0.80[EUR][1000 genomes]
rs10936130	0.86[EUR][1000 genomes]
rs10936138	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12486595	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12487873	0.85[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs12487933	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491983	0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs12493753	0.86[EUR][1000 genomes]
rs12496739	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12631828	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631832	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12634966	0.86[EUR][1000 genomes]
rs12635395	0.80[EUR][1000 genomes]
rs12635963	0.86[EUR][1000 genomes]
rs12637243	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12637436	0.89[EUR][1000 genomes]
rs12638258	0.85[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs1320239	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1435638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1435639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16829007	0.81[YRI][hapmap]
rs16829072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16829079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16829116	0.87[AMR][1000 genomes]
rs17486183	0.80[EUR][1000 genomes]
rs17627838	0.86[EUR][1000 genomes]
rs2140982	0.80[EUR][1000 genomes]
rs2363654	0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2363657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28491830	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28669117	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4021884	0.86[EUR][1000 genomes]
rs4432589	0.80[EUR][1000 genomes]
rs4522814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5025785	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56019559	0.80[EUR][1000 genomes]
rs56130447	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56303915	0.86[EUR][1000 genomes]
rs58034569	0.89[AMR][1000 genomes]
rs59112782	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59502510	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59661293	0.80[EUR][1000 genomes]
rs60566034	0.80[EUR][1000 genomes]
rs60921365	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67074371	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6762774	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6769314	0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6770005	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775960	0.93[YRI][hapmap]
rs6789607	0.85[YRI][hapmap]
rs6795710	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6797871	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6801076	0.83[YRI][hapmap]
rs6804401	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6806720	0.86[EUR][1000 genomes]
rs6810324	0.93[YRI][hapmap]
rs73020715	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73020720	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022714	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73022726	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73022742	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73166394	0.80[EUR][1000 genomes]
rs73166397	0.80[EUR][1000 genomes]
rs73166399	0.80[EUR][1000 genomes]
rs73168703	0.80[EUR][1000 genomes]
rs73168704	0.80[EUR][1000 genomes]
rs73168713	0.80[EUR][1000 genomes]
rs73168718	0.80[EUR][1000 genomes]
rs73168720	0.80[EUR][1000 genomes]
rs73168737	0.80[EUR][1000 genomes]
rs73170313	0.86[EUR][1000 genomes]
rs73170316	0.86[EUR][1000 genomes]
rs73170323	0.86[EUR][1000 genomes]
rs73170340	0.86[EUR][1000 genomes]
rs73170342	0.86[EUR][1000 genomes]
rs73170344	0.86[EUR][1000 genomes]
rs73170358	0.86[EUR][1000 genomes]
rs73170365	0.86[EUR][1000 genomes]
rs73170367	0.86[EUR][1000 genomes]
rs73170369	0.86[EUR][1000 genomes]
rs73170394	0.86[EUR][1000 genomes]
rs73170401	0.86[EUR][1000 genomes]
rs73172109	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73172118	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73172122	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73172127	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7618252	0.93[YRI][hapmap]
rs7619886	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638518	0.89[AMR][1000 genomes]
rs7638606	0.89[AMR][1000 genomes]
rs939116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs951113	0.80[EUR][1000 genomes]
rs9681065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810400	0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs9811282	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812307	0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9815348	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9819130	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830994	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9849688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854620	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9858498	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861322	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[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	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1013046	chr3:158176582-158244606	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1014557	chr3:158176582-158251602	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv3446075	chr3:158214299-158241785	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs939115	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158237600-158239600	Enhancers	NHDF-Ad	bronchial
2	chr3:158237800-158241400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:158238000-158239400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:158238000-158239400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:158238200-158240200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:158238600-158240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:158238600-158240200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:158238600-158240200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:158239200-158239800	Weak transcription	Osteobl	bone

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