Variant report

Variant	rs12638258
Chromosome Location	chr3:158096434-158096435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10513526	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10936130	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12487004	0.85[CHB][hapmap]
rs12487397	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12487873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487933	0.82[EUR][1000 genomes]
rs12490116	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs12491983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12493633	0.89[EUR][1000 genomes]
rs12493753	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12495621	0.87[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs12496739	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12497109	0.89[EUR][1000 genomes]
rs12497273	0.89[EUR][1000 genomes]
rs12631828	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12631832	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12634372	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12634405	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12634483	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12634966	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635395	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12635963	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637243	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12637436	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1320239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1435638	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1435639	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs16829072	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs16829079	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs17486183	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17627838	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17683721	0.87[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs17683787	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs2140982	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2176890	0.88[EUR][1000 genomes]
rs2363654	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2363657	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs28669117	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28781280	0.89[EUR][1000 genomes]
rs4021884	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4432589	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4522814	0.82[EUR][1000 genomes]
rs5025785	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55818809	0.89[EUR][1000 genomes]
rs56019559	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56101139	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56130447	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56303915	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59112782	0.87[EUR][1000 genomes]
rs59661293	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60463398	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60566034	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60921365	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61244743	0.89[EUR][1000 genomes]
rs67074371	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6762774	0.91[EUR][1000 genomes]
rs6769314	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770005	0.87[EUR][1000 genomes]
rs6804401	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6806720	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73020715	0.88[EUR][1000 genomes]
rs73020720	0.88[EUR][1000 genomes]
rs73166334	0.89[EUR][1000 genomes]
rs73166338	0.89[EUR][1000 genomes]
rs73166343	0.89[EUR][1000 genomes]
rs73166347	0.89[EUR][1000 genomes]
rs73166351	0.88[EUR][1000 genomes]
rs73166352	0.89[EUR][1000 genomes]
rs73166357	0.89[EUR][1000 genomes]
rs73166361	0.87[EUR][1000 genomes]
rs73166362	0.89[EUR][1000 genomes]
rs73166370	0.89[EUR][1000 genomes]
rs73166374	0.89[EUR][1000 genomes]
rs73166375	0.89[EUR][1000 genomes]
rs73166381	0.89[EUR][1000 genomes]
rs73166383	0.89[EUR][1000 genomes]
rs73166386	0.89[EUR][1000 genomes]
rs73166387	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73166388	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73166390	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73166394	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73166397	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73166399	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73168703	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73168704	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73168713	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73168718	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73168720	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73168737	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73170313	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170316	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170323	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170340	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170342	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170344	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170358	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170365	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170367	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170369	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170394	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73172109	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73172118	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73172122	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73172127	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7619886	0.87[EUR][1000 genomes]
rs7650062	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs939115	0.85[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs939116	0.80[EUR][1000 genomes]
rs951113	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9681065	0.85[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs9810400	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9811282	0.87[EUR][1000 genomes]
rs9812307	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9815348	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9819130	0.82[EUR][1000 genomes]
rs9849688	0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs9854620	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9858498	0.87[EUR][1000 genomes]
rs9861322	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	nsv1000904	chr3:158094357-158159317	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12638258	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158096000-158096600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:158096400-158096800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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