Variant report

Variant	rs6804401
Chromosome Location	chr3:158194931-158194932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158193823..158196386-chr3:158204544..158206278,2	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10513526	0.86[EUR][1000 genomes]
rs10936130	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12486595	0.94[AMR][1000 genomes]
rs12487004	0.86[AMR][1000 genomes]
rs12487397	0.84[EUR][1000 genomes]
rs12487873	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12487933	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12490116	0.84[EUR][1000 genomes]
rs12491983	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12493633	0.84[EUR][1000 genomes]
rs12493753	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496739	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12497109	0.84[EUR][1000 genomes]
rs12497273	0.84[EUR][1000 genomes]
rs12631828	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12631832	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634372	0.84[EUR][1000 genomes]
rs12634405	0.84[EUR][1000 genomes]
rs12634483	0.83[EUR][1000 genomes]
rs12634966	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12635395	0.86[EUR][1000 genomes]
rs12635963	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12637243	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12637436	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12638258	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1435638	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1435639	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16829072	0.94[AMR][1000 genomes]
rs16829079	0.94[AMR][1000 genomes]
rs16829116	0.87[AMR][1000 genomes]
rs17486183	0.86[EUR][1000 genomes]
rs17627838	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17683721	0.84[EUR][1000 genomes]
rs17683787	0.84[EUR][1000 genomes]
rs2140982	0.86[EUR][1000 genomes]
rs2363654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363657	0.94[AMR][1000 genomes]
rs28491830	0.86[AMR][1000 genomes]
rs28669117	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28781280	0.84[EUR][1000 genomes]
rs4021884	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4432589	0.86[EUR][1000 genomes]
rs4522814	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5025785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55818809	0.84[EUR][1000 genomes]
rs56019559	0.86[EUR][1000 genomes]
rs56101139	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56130447	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56303915	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58034569	0.89[AMR][1000 genomes]
rs59112782	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59502510	0.93[AMR][1000 genomes]
rs59661293	0.86[EUR][1000 genomes]
rs60463398	0.86[EUR][1000 genomes]
rs60566034	0.86[EUR][1000 genomes]
rs60921365	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67074371	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762774	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6769314	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6795710	0.94[AMR][1000 genomes]
rs6797871	0.93[AMR][1000 genomes]
rs6806720	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73020715	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73020720	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73022714	0.94[AMR][1000 genomes]
rs73022726	0.94[AMR][1000 genomes]
rs73022742	0.94[AMR][1000 genomes]
rs73030514	0.81[AFR][1000 genomes]
rs73166351	0.83[EUR][1000 genomes]
rs73166352	0.84[EUR][1000 genomes]
rs73166357	0.84[EUR][1000 genomes]
rs73166361	0.82[EUR][1000 genomes]
rs73166362	0.84[EUR][1000 genomes]
rs73166370	0.84[EUR][1000 genomes]
rs73166374	0.84[EUR][1000 genomes]
rs73166375	0.84[EUR][1000 genomes]
rs73166381	0.84[EUR][1000 genomes]
rs73166383	0.84[EUR][1000 genomes]
rs73166386	0.84[EUR][1000 genomes]
rs73166387	0.84[EUR][1000 genomes]
rs73166388	0.84[EUR][1000 genomes]
rs73166390	0.84[EUR][1000 genomes]
rs73166394	0.86[EUR][1000 genomes]
rs73166397	0.86[EUR][1000 genomes]
rs73166399	0.86[EUR][1000 genomes]
rs73168703	0.86[EUR][1000 genomes]
rs73168704	0.86[EUR][1000 genomes]
rs73168713	0.86[EUR][1000 genomes]
rs73168718	0.86[EUR][1000 genomes]
rs73168720	0.86[EUR][1000 genomes]
rs73168737	0.86[EUR][1000 genomes]
rs73170313	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170316	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170323	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170340	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170342	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170344	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170358	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170365	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73170367	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73170369	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73170394	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73170401	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73172109	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73172118	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73172122	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73172127	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73172146	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7618252	0.81[AFR][1000 genomes]
rs7619886	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7638518	0.89[AMR][1000 genomes]
rs7638606	0.89[AMR][1000 genomes]
rs939115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs939116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs951113	0.86[EUR][1000 genomes]
rs9681065	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9811282	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812307	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815348	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819130	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9830994	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9849688	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9854620	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858498	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9861322	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6804401	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158190200-158201000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:158190600-158195600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:158194000-158203800	Weak transcription	Fetal Heart	heart

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