Variant report

Variant	rs12486595
Chromosome Location	chr3:158270000-158270001
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	chr3:158269405..158273514-chr3:158275272..158279409,4	K562	blood:
2	chr3:158264437..158266302-chr3:158268722..158271575,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10154981	0.88[EUR][1000 genomes]
rs10154986	0.89[EUR][1000 genomes]
rs1038885	0.86[EUR][1000 genomes]
rs10513527	0.90[EUR][1000 genomes]
rs12106885	0.91[EUR][1000 genomes]
rs12107742	0.91[EUR][1000 genomes]
rs12487004	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487933	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12496739	0.87[AMR][1000 genomes]
rs12631828	0.85[AMR][1000 genomes]
rs12631832	0.87[AMR][1000 genomes]
rs12637243	0.89[AMR][1000 genomes]
rs12638363	0.82[EUR][1000 genomes]
rs13315529	0.89[EUR][1000 genomes]
rs13318109	0.91[EUR][1000 genomes]
rs1435638	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435639	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829072	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829079	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829116	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16829135	0.89[EUR][1000 genomes]
rs16829273	0.82[EUR][1000 genomes]
rs16829283	0.82[EUR][1000 genomes]
rs17630223	0.84[EUR][1000 genomes]
rs17630785	0.81[EUR][1000 genomes]
rs17631016	0.82[EUR][1000 genomes]
rs17631078	0.82[EUR][1000 genomes]
rs1864502	0.84[EUR][1000 genomes]
rs2082838	0.89[EUR][1000 genomes]
rs2115942	0.91[EUR][1000 genomes]
rs2291594	0.84[EUR][1000 genomes]
rs2363654	0.94[AMR][1000 genomes]
rs2363657	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364273	0.91[EUR][1000 genomes]
rs28491830	0.91[ASN][1000 genomes]
rs28669117	0.94[AMR][1000 genomes]
rs28856044	0.91[EUR][1000 genomes]
rs3806642	0.84[EUR][1000 genomes]
rs3817373	0.91[EUR][1000 genomes]
rs41272617	0.89[EUR][1000 genomes]
rs4368546	0.88[EUR][1000 genomes]
rs4522814	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025785	0.94[AMR][1000 genomes]
rs56130447	0.89[AMR][1000 genomes]
rs56321207	0.82[EUR][1000 genomes]
rs56973279	0.86[EUR][1000 genomes]
rs58034569	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58878998	0.85[EUR][1000 genomes]
rs59112782	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59502510	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59527167	0.84[EUR][1000 genomes]
rs59602208	0.84[EUR][1000 genomes]
rs59973861	0.91[EUR][1000 genomes]
rs60921365	0.87[AMR][1000 genomes]
rs61107068	0.82[EUR][1000 genomes]
rs61292339	0.91[EUR][1000 genomes]
rs67074371	0.98[AMR][1000 genomes]
rs6762774	0.87[AMR][1000 genomes]
rs6769314	0.98[AMR][1000 genomes]
rs6770005	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6779054	0.89[EUR][1000 genomes]
rs6792976	0.88[EUR][1000 genomes]
rs6795710	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797871	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804401	0.94[AMR][1000 genomes]
rs73020715	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73020720	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73022714	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022742	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022762	0.91[EUR][1000 genomes]
rs73022770	0.91[EUR][1000 genomes]
rs73022798	0.91[EUR][1000 genomes]
rs73024783	0.89[EUR][1000 genomes]
rs73024790	0.89[EUR][1000 genomes]
rs73028934	0.84[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];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638518	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7638606	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs939115	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs939116	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9681065	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9811282	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812307	0.89[AMR][1000 genomes]
rs9815348	0.94[AMR][1000 genomes]
rs9819130	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830994	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849437	0.91[EUR][1000 genomes]
rs9849688	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9854620	0.94[AMR][1000 genomes]
rs9858498	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9861322	0.80[ASN][1000 genomes]
rs9872682	0.90[EUR][1000 genomes]
rs9881679	0.91[EUR][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	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
5	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
6	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
7	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
rs12486595	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158256600-158280000	Weak transcription	K562	blood
2	chr3:158259800-158270000	Weak transcription	Ovary	ovary
3	chr3:158260000-158279200	Weak transcription	Left Ventricle	heart
4	chr3:158260400-158270600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:158265800-158270400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:158269800-158270200	Active TSS	HepG2	liver

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