Variant report

Variant	rs16829072
Chromosome Location	chr3:158250154-158250155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:157324285..157324887-chr3:158249956..158250485,2	MCF-7	breast:
2	chr3:158248140..158250406-chr3:158251926..158254670,2	K562	blood:
3	chr3:158151947..158152666-chr3:158249618..158250586,2	MCF-7	breast:
4	chr3:157978531..157979431-chr3:158249670..158250340,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10154981	0.86[EUR][1000 genomes]
rs10154986	0.87[EUR][1000 genomes]
rs1038885	0.85[EUR][1000 genomes]
rs10513527	0.83[YRI][hapmap];0.88[EUR][1000 genomes]
rs10936138	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12106885	0.89[EUR][1000 genomes]
rs12107742	0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs12486595	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487873	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs12487933	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491983	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12496739	0.87[AMR][1000 genomes]
rs12631828	0.85[AMR][1000 genomes]
rs12631832	0.82[CHB][hapmap];0.87[AMR][1000 genomes]
rs12637243	0.89[AMR][1000 genomes]
rs12638258	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12638363	0.80[EUR][1000 genomes]
rs1320239	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs13315529	0.87[EUR][1000 genomes]
rs13318109	0.89[EUR][1000 genomes]
rs1435638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829079	1.00[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]
rs16829116	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16829118	0.91[YRI][hapmap]
rs16829135	0.87[EUR][1000 genomes]
rs16829273	0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs16829283	0.80[EUR][1000 genomes]
rs17630223	0.82[EUR][1000 genomes]
rs17631016	0.80[EUR][1000 genomes]
rs17631078	0.80[EUR][1000 genomes]
rs1864502	0.82[EUR][1000 genomes]
rs2082838	0.87[EUR][1000 genomes]
rs2115942	0.89[EUR][1000 genomes]
rs2291594	0.82[EUR][1000 genomes]
rs2363654	0.85[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes]
rs2363657	1.00[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]
rs2364273	0.89[EUR][1000 genomes]
rs28491830	0.91[ASN][1000 genomes]
rs28669117	0.94[AMR][1000 genomes]
rs28856044	0.89[EUR][1000 genomes]
rs3806642	0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs3817373	0.89[EUR][1000 genomes]
rs41272617	0.87[EUR][1000 genomes]
rs4368546	0.86[EUR][1000 genomes]
rs4522814	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025785	0.94[AMR][1000 genomes]
rs56130447	0.89[AMR][1000 genomes]
rs56321207	0.80[EUR][1000 genomes]
rs56973279	0.85[EUR][1000 genomes]
rs58034569	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58878998	0.83[EUR][1000 genomes]
rs59112782	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59502510	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59527167	0.82[EUR][1000 genomes]
rs59602208	0.82[EUR][1000 genomes]
rs59973861	0.89[EUR][1000 genomes]
rs60921365	0.87[AMR][1000 genomes]
rs61107068	0.80[EUR][1000 genomes]
rs61292339	0.89[EUR][1000 genomes]
rs67074371	0.98[AMR][1000 genomes]
rs6762774	0.87[AMR][1000 genomes]
rs6769314	0.85[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes]
rs6770005	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6779054	0.87[EUR][1000 genomes]
rs6792976	0.86[EUR][1000 genomes]
rs6795710	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797871	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804401	0.94[AMR][1000 genomes]
rs73020715	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73020720	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73022714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022726	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022742	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022762	0.89[EUR][1000 genomes]
rs73022770	0.89[EUR][1000 genomes]
rs73022798	0.89[EUR][1000 genomes]
rs73024783	0.87[EUR][1000 genomes]
rs73024790	0.87[EUR][1000 genomes]
rs73028934	0.82[EUR][1000 genomes]
rs73172109	0.82[AMR][1000 genomes]
rs73172118	0.91[AMR][1000 genomes]
rs73172122	0.89[AMR][1000 genomes]
rs73172127	0.92[AMR][1000 genomes]
rs7619886	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638518	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7638606	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs939115	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]
rs939116	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9681065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9810400	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9811282	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812307	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes]
rs9815348	0.94[AMR][1000 genomes]
rs9819130	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830994	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849437	0.89[EUR][1000 genomes]
rs9849688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9854620	0.94[AMR][1000 genomes]
rs9858498	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9861322	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9872682	0.88[EUR][1000 genomes]
rs9881679	0.89[EUR][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	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
5	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
6	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
7	nsv916167	chr3:158240540-158320581	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16829072	GFM1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158246600-158261000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr3:158249400-158264400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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