Variant report

Variant	rs6740054
Chromosome Location	chr2:99576631-99576632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10165534	0.84[EUR][1000 genomes]
rs10167390	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10170063	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10179043	0.90[CEU][hapmap]
rs10179910	0.82[EUR][1000 genomes]
rs10181344	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10181422	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10190421	0.90[CEU][hapmap]
rs10193019	0.81[EUR][1000 genomes]
rs10196680	0.84[EUR][1000 genomes]
rs10202452	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1115756	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1115757	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1133977	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs1133978	0.81[ASN][1000 genomes]
rs11683107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs11683188	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11688004	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs11692336	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11895749	0.83[ASN][1000 genomes]
rs11903311	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12464710	0.84[EUR][1000 genomes]
rs12467679	0.83[EUR][1000 genomes]
rs12468807	0.90[CEU][hapmap]
rs12470471	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12473029	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs12475034	0.83[CEU][hapmap]
rs12477754	0.84[EUR][1000 genomes]
rs12477978	0.90[EUR][1000 genomes]
rs12613624	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs12619780	0.84[ASN][1000 genomes]
rs12987548	0.83[ASN][1000 genomes]
rs13000731	0.81[ASN][1000 genomes]
rs13008171	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs13033012	0.81[ASN][1000 genomes]
rs13396358	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13407840	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13412764	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1349778	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs1349779	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs1453561	0.90[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs1453562	0.90[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs1453563	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs1453564	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530996	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1563106	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1563107	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1563108	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1580068	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs17708218	0.90[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs17708262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17759607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs1993230	0.90[CEU][hapmap]
rs2045057	0.90[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs2084988	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2123686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2309524	0.90[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2516830	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2516833	0.82[ASN][1000 genomes]
rs2516835	0.83[ASN][1000 genomes]
rs2632283	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs28575117	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28648058	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34272114	0.83[ASN][1000 genomes]
rs35001733	0.82[EUR][1000 genomes]
rs4324365	0.90[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs4346438	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4374423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4585080	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4622780	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4850897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4851179	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851184	0.90[CEU][hapmap]
rs4851185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4851188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs62154638	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62156558	0.83[AMR][1000 genomes]
rs6542846	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542852	0.85[EUR][1000 genomes]
rs6542858	0.81[EUR][1000 genomes]
rs6542866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs6542868	0.83[ASN][1000 genomes]
rs6704766	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs6707462	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6721535	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6722164	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6724476	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6727749	0.81[ASN][1000 genomes]
rs6732579	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6733285	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs6735801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6736064	0.83[EUR][1000 genomes]
rs6737257	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6740035	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6740267	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6750876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6753650	0.84[ASN][1000 genomes]
rs6754843	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6756880	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6757019	0.90[CEU][hapmap]
rs6759354	0.84[EUR][1000 genomes]
rs720229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs72957109	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7558239	0.84[EUR][1000 genomes]
rs7570657	0.81[CHB][hapmap];0.81[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7571390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7586608	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7588059	0.89[ASN][1000 genomes]
rs7591794	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7599427	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7605734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7606635	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7608938	0.83[ASN][1000 genomes]
rs896886	0.90[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs9308816	0.90[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs9710648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs972768	0.90[CEU][hapmap]
rs9808541	0.90[CEU][hapmap];0.84[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	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	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
4	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6740054	LIPT1	cis	lymphoblastoid	seeQTL
rs6740054	TSGA10	cis	cerebellum	SCAN
rs6740054	TSGA10	cis	Thyroid	GTEx
rs6740054	FAM178B	cis	cerebellum	SCAN
rs6740054	LIPT1	cis	multi-tissue	Pritchard
rs6740054	TSGA10	cis	Lymphoblastoid	GTEx
rs6740054	ZAP70	cis	parietal	SCAN
rs6740054	LIPT1	cis	parietal	SCAN
rs6740054	TSGA10	cis	lymphoblastoid	seeQTL
rs6740054	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs6740054	TSGA10	cis	multi-tissue	Pritchard
rs6740054	LIPT1	cis	cerebellum	SCAN
rs6740054	TSGA10	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99575600-99577200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:99575800-99576800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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