Variant report

Variant	rs12468024
Chromosome Location	chr2:99495980-99495981
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	chr2:99495810..99498238-chr2:99499497..99501291,2	MCF-7	breast:
2	chr2:99492447..99494949-chr2:99495015..99496598,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10169003	0.94[EUR][1000 genomes]
rs10172158	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10178956	0.96[ASN][1000 genomes]
rs10181972	0.94[EUR][1000 genomes]
rs10188156	0.88[EUR][1000 genomes]
rs11123755	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11887536	0.91[EUR][1000 genomes]
rs11893888	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12474283	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12712033	0.85[JPT][hapmap]
rs12712035	0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs12712036	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs12712038	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712039	0.89[EUR][1000 genomes]
rs12712041	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12712043	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13004700	0.85[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13004923	0.94[EUR][1000 genomes]
rs13005124	0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13011428	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025076	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13025913	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13028500	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1356424	0.80[EUR][1000 genomes]
rs1581250	0.94[EUR][1000 genomes]
rs1581251	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1607256	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17758170	0.81[CEU][hapmap]
rs1878585	0.94[EUR][1000 genomes]
rs1976766	0.89[AMR][1000 genomes]
rs1983352	0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs2280256	0.83[EUR][1000 genomes]
rs4263159	0.81[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs4311103	0.82[CHB][hapmap]
rs4850888	0.87[EUR][1000 genomes]
rs4850889	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851162	0.88[EUR][1000 genomes]
rs4851163	0.88[EUR][1000 genomes]
rs4851167	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851170	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851171	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851173	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851177	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56125264	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6419564	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6542838	0.81[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs6542839	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6542841	0.82[CEU][hapmap]
rs6542843	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6711022	0.83[EUR][1000 genomes]
rs6713991	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs6714243	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6717372	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6719634	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6724477	0.81[CEU][hapmap]
rs6726156	0.83[EUR][1000 genomes]
rs6739176	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6739503	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6757098	0.84[CEU][hapmap]
rs6760065	0.84[CEU][hapmap]
rs7423519	0.81[CEU][hapmap]
rs7579189	0.81[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs7608889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883773	0.82[CEU][hapmap]
rs925887	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs981601	0.81[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs981602	0.80[CEU][hapmap];0.84[JPT][hapmap];0.87[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12468024	TSGA10	cis	Lymphoblastoid	GTEx

Chromatin state (count:6 , 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	chr2:99488200-99497200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:99490200-99497200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:99491000-99496800	Weak transcription	Esophagus	oesophagus
6	chr2:99492000-99500400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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