Variant report

Variant	rs12712039
Chromosome Location	chr2:99497980-99497981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99482631..99484233-chr2:99497565..99499483,2	MCF-7	breast:
2	chr2:99495810..99498238-chr2:99499497..99501291,2	MCF-7	breast:
3	chr2:99496861..99499359-chr2:99536872..99539467,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10169003	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10172158	0.89[EUR][1000 genomes]
rs10175560	0.83[ASN][1000 genomes]
rs10181972	0.95[EUR][1000 genomes]
rs10188156	0.86[EUR][1000 genomes]
rs11123755	0.89[EUR][1000 genomes]
rs11123756	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11887536	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11893888	0.94[EUR][1000 genomes]
rs11900176	0.83[ASN][1000 genomes]
rs11900524	0.81[ASN][1000 genomes]
rs12468024	0.89[EUR][1000 genomes]
rs12478574	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12712035	0.85[EUR][1000 genomes]
rs12712036	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12712037	0.83[ASN][1000 genomes]
rs12712038	0.89[EUR][1000 genomes]
rs12990579	0.83[ASN][1000 genomes]
rs13004923	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13005148	0.86[ASN][1000 genomes]
rs13006398	0.81[AMR][1000 genomes]
rs13024838	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1568213	0.85[EUR][1000 genomes]
rs1581249	0.95[ASN][1000 genomes]
rs1581250	0.95[EUR][1000 genomes]
rs1581251	0.89[EUR][1000 genomes]
rs1878585	0.95[EUR][1000 genomes]
rs1878589	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1962029	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1983352	0.85[EUR][1000 genomes]
rs2280256	0.82[EUR][1000 genomes]
rs4263159	0.86[EUR][1000 genomes]
rs4499468	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4553869	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4850888	0.85[EUR][1000 genomes]
rs4851162	0.86[EUR][1000 genomes]
rs4851163	0.86[EUR][1000 genomes]
rs4851167	0.89[EUR][1000 genomes]
rs4851170	0.89[EUR][1000 genomes]
rs4851171	0.89[EUR][1000 genomes]
rs6542838	0.86[EUR][1000 genomes]
rs6542839	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6542841	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6704682	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6711022	0.82[EUR][1000 genomes]
rs6713991	0.86[EUR][1000 genomes]
rs6714243	0.89[EUR][1000 genomes]
rs6717372	0.87[EUR][1000 genomes]
rs6719634	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6726156	0.82[EUR][1000 genomes]
rs6752025	0.86[AFR][1000 genomes]
rs6757098	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6760065	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7423519	0.81[ASN][1000 genomes]
rs7565510	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7565614	0.83[ASN][1000 genomes]
rs7565736	0.83[ASN][1000 genomes]
rs7565819	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7579189	0.86[EUR][1000 genomes]
rs7588441	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7590596	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7608889	0.89[EUR][1000 genomes]
rs883773	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs925887	0.82[EUR][1000 genomes]
rs981601	0.86[EUR][1000 genomes]
rs981602	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:99487600-99499400	Weak transcription	Gastric	stomach
3	chr2:99492000-99500400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:99496800-99501800	Enhancers	Esophagus	oesophagus
5	chr2:99497200-99498400	Enhancers	NHEK	skin
6	chr2:99497200-99499400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:99497400-99498200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:99497800-99505600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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