Variant report

Variant	rs12536959
Chromosome Location	chr7:78326526-78326527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10228359	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10228963	1.00[CEU][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10229438	1.00[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10229458	1.00[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10230190	1.00[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10230478	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10230501	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10231465	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10233033	0.85[EUR][1000 genomes]
rs10243772	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10243883	1.00[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10256389	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10272085	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10273632	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10953681	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10953686	1.00[CEU][hapmap]
rs10953687	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11760430	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11763541	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11764280	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11768142	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11768372	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11768397	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11770561	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11770565	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11772790	0.85[EUR][1000 genomes]
rs11773249	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12530747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][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]
rs12530771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530773	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12530792	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12531353	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12531547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533182	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12533194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534669	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12534800	1.00[CEU][hapmap]
rs12535118	0.91[EUR][1000 genomes]
rs12536628	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12536952	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12537842	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12538564	0.87[CEU][hapmap]
rs12538687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539657	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12540478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540572	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12540597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12669245	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13240011	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1496765	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17441871	1.00[CEU][hapmap]
rs17442142	1.00[CEU][hapmap]
rs28502814	0.80[EUR][1000 genomes]
rs28565439	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28650857	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35895217	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4370470	1.00[CEU][hapmap]
rs55669940	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55827541	0.85[EUR][1000 genomes]
rs55984124	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56161537	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56165236	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56277847	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66495951	0.81[EUR][1000 genomes]
rs6946747	0.85[EUR][1000 genomes]
rs6953739	1.00[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs73135509	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73135518	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73135526	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73145166	0.94[EUR][1000 genomes]
rs73145170	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73145178	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73145192	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73145196	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73145199	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73147023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73147024	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73147031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73147034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73147035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73147039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73147058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73149076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73149082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73149083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73149085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73149086	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73149096	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73150705	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73150708	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73150717	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73150732	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73150760	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73150764	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73150767	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73150783	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73150785	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73150787	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73150791	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73150794	0.85[EUR][1000 genomes]
rs73152411	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73152421	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73152427	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73152434	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73152443	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73152448	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv888509	chr7:78307944-78327299	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
4	nsv1019355	chr7:78319575-78399845	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12536959	SGCE	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78313800-78334200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:78318000-78326800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:78318400-78327400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:78322200-78328800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:78326200-78327600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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