Variant report

Variant	rs12712043
Chromosome Location	chr2:99541494-99541495
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	chr2:99525536..99528520-chr2:99541090..99543085,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10169003	0.80[EUR][1000 genomes]
rs10172158	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10181972	0.80[EUR][1000 genomes]
rs10192266	0.80[AFR][1000 genomes]
rs11123755	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12468024	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12474283	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12712038	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12712041	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12712042	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13004700	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13004923	0.80[EUR][1000 genomes]
rs13005124	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13011428	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13025076	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13025913	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13028500	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1581250	0.80[EUR][1000 genomes]
rs1581251	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1607256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1878585	0.80[EUR][1000 genomes]
rs1976766	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2048949	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4311103	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4850889	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4850890	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4851167	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4851170	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4851171	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4851173	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851174	0.81[AMR][1000 genomes]
rs4851175	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4851176	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4851177	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56125264	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6419564	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542843	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542845	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6714243	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6717372	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6724477	0.83[AMR][1000 genomes]
rs6739176	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6739503	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6742047	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7608889	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs908672	0.85[AFR][1000 genomes]
rs925887	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[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	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
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12712043	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs12712043	TSGA10	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99532400-99542800	Weak transcription	Pancreas	Pancrea
2	chr2:99538000-99550800	Weak transcription	Gastric	stomach
3	chr2:99538400-99542600	Weak transcription	NHEK	skin
4	chr2:99538400-99551400	Weak transcription	Esophagus	oesophagus
5	chr2:99540600-99541800	Enhancers	Fetal Intestine Small	intestine
6	chr2:99540600-99542000	Enhancers	Fetal Intestine Large	intestine
7	chr2:99540600-99542800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:99541400-99541600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:99541400-99541800	Enhancers	Primary neutrophils fromperipheralblood	blood

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