Variant report

Variant	rs12496739
Chromosome Location	chr3:158169959-158169960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158165380..158167229-chr3:158167720..158170600,2	MCF-7	breast:
2	chr15:72523089..72524657-chr3:158169373..158172267,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067225	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10513526	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs10936130	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10936138	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12486595	0.87[AMR][1000 genomes]
rs12487397	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12487873	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12487933	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12490116	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12491983	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12493633	0.87[EUR][1000 genomes]
rs12493753	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12497109	0.87[EUR][1000 genomes]
rs12497273	0.87[EUR][1000 genomes]
rs12631828	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12631832	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12634372	0.86[EUR][1000 genomes]
rs12634405	0.87[EUR][1000 genomes]
rs12634483	0.85[EUR][1000 genomes]
rs12634966	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12635395	0.89[EUR][1000 genomes]
rs12635963	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637243	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12637436	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12638258	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1320239	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1435638	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1435639	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16829072	0.87[AMR][1000 genomes]
rs16829079	0.87[AMR][1000 genomes]
rs17486183	0.89[EUR][1000 genomes]
rs17627838	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17683721	0.86[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs17683787	0.87[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs2140982	0.89[EUR][1000 genomes]
rs2176890	0.85[EUR][1000 genomes]
rs2363654	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2363657	0.87[AMR][1000 genomes]
rs28669117	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28781280	0.87[EUR][1000 genomes]
rs4021884	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4432589	0.89[EUR][1000 genomes]
rs4522814	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5025785	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55818809	0.87[EUR][1000 genomes]
rs56019559	0.89[EUR][1000 genomes]
rs56101139	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56130447	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56303915	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59112782	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59502510	0.85[AMR][1000 genomes]
rs59661293	0.89[EUR][1000 genomes]
rs60463398	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs60566034	0.89[EUR][1000 genomes]
rs60921365	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61244743	0.87[EUR][1000 genomes]
rs67074371	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6762774	0.97[EUR][1000 genomes]
rs6769314	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6770005	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6795710	0.87[AMR][1000 genomes]
rs6797871	0.85[AMR][1000 genomes]
rs6804401	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806720	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73020715	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73020720	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73022714	0.87[AMR][1000 genomes]
rs73022726	0.87[AMR][1000 genomes]
rs73022742	0.87[AMR][1000 genomes]
rs73166334	0.87[EUR][1000 genomes]
rs73166338	0.87[EUR][1000 genomes]
rs73166343	0.87[EUR][1000 genomes]
rs73166347	0.87[EUR][1000 genomes]
rs73166351	0.85[EUR][1000 genomes]
rs73166352	0.87[EUR][1000 genomes]
rs73166357	0.87[EUR][1000 genomes]
rs73166361	0.85[EUR][1000 genomes]
rs73166362	0.87[EUR][1000 genomes]
rs73166370	0.87[EUR][1000 genomes]
rs73166374	0.87[EUR][1000 genomes]
rs73166375	0.87[EUR][1000 genomes]
rs73166381	0.87[EUR][1000 genomes]
rs73166383	0.87[EUR][1000 genomes]
rs73166386	0.87[EUR][1000 genomes]
rs73166387	0.87[EUR][1000 genomes]
rs73166388	0.87[EUR][1000 genomes]
rs73166390	0.87[EUR][1000 genomes]
rs73166394	0.89[EUR][1000 genomes]
rs73166397	0.89[EUR][1000 genomes]
rs73166399	0.89[EUR][1000 genomes]
rs73168703	0.89[EUR][1000 genomes]
rs73168704	0.89[EUR][1000 genomes]
rs73168713	0.89[EUR][1000 genomes]
rs73168718	0.89[EUR][1000 genomes]
rs73168720	0.89[EUR][1000 genomes]
rs73168737	0.89[EUR][1000 genomes]
rs73170313	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73170316	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73170323	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73170340	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73170342	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73170344	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73170358	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73170365	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73170367	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73170369	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73170394	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73170401	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73172109	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73172118	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73172122	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73172127	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73172146	0.85[EUR][1000 genomes]
rs7619886	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7650062	0.87[EUR][1000 genomes]
rs939115	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs939116	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs951113	0.89[EUR][1000 genomes]
rs9681065	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9810400	0.93[CEU][hapmap]
rs9811282	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9812307	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9815348	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9819130	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9830994	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9849688	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9854620	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9858498	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9861322	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	nsv967206	chr3:158149860-158176292	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12496739	GFM1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158156400-158176200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:158161800-158171800	Weak transcription	GM12878-XiMat	blood
3	chr3:158165600-158172600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:158169200-158176000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:158169400-158170000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr3:158169400-158170000	Enhancers	HepG2	liver
7	chr3:158169400-158171400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:158169600-158171200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:158169600-158182400	Weak transcription	Primary B cells from cord blood	blood

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