Variant report

Variant	rs16945974
Chromosome Location	chr16:48256602-48256603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10163354	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs10163462	0.85[ASN][1000 genomes]
rs10521167	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11076564	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11859911	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11861031	0.85[ASN][1000 genomes]
rs11861127	0.83[CHD][hapmap]
rs11861348	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11861379	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11863133	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11863233	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11863236	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11863325	0.85[ASN][1000 genomes]
rs11863414	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11865596	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11866225	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11866251	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs11866312	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11866529	1.00[CHD][hapmap]
rs13331031	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13332304	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13334052	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13334480	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs13335504	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs13336542	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13336625	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13336759	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13337955	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13338105	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16945916	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs16945917	0.85[ASN][1000 genomes]
rs16945919	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs16945972	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16945988	0.83[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16945990	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16946006	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16946011	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16946014	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16946122	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs17743256	0.85[ASN][1000 genomes]
rs2129245	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs28376623	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28503414	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28515165	0.85[EUR][1000 genomes]
rs28605399	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28626252	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28654935	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28684834	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28696036	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28842015	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28849445	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41280939	0.85[ASN][1000 genomes]
rs4325548	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4340327	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5017203	0.99[EUR][1000 genomes]
rs57912486	0.85[ASN][1000 genomes]
rs58938063	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60431412	0.96[EUR][1000 genomes]
rs62058521	0.85[ASN][1000 genomes]
rs62058522	0.85[ASN][1000 genomes]
rs62058526	0.85[ASN][1000 genomes]
rs62058528	0.85[ASN][1000 genomes]
rs7184452	0.87[EUR][1000 genomes]
rs7184831	0.85[ASN][1000 genomes]
rs7186982	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7187166	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7187233	0.85[ASN][1000 genomes]
rs7191181	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7191844	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs7195606	1.00[CEU][hapmap]
rs7202089	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7203378	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7203432	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7203695	0.85[ASN][1000 genomes]
rs7206909	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs73540901	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73542903	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73542904	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73546434	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546437	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546439	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73555628	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73555630	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73555643	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7359477	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74018300	0.85[ASN][1000 genomes]
rs8043685	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8043751	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8047091	1.00[CHD][hapmap]
rs8047397	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8049398	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8050120	0.85[ASN][1000 genomes]
rs8051016	0.85[CHD][hapmap]
rs8051205	1.00[CHD][hapmap]
rs8051546	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8051852	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8054117	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8054444	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8055128	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056100	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056143	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056692	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8058396	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8060696	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8060722	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062407	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs957881	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs9926206	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9927756	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs9932328	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9934833	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9935854	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs9938414	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9939742	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs9941123	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]

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	nsv1059259	chr16:48113396-48304404	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv542916	chr16:48113396-48304404	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16945974	GPT2	cis	parietal	SCAN
rs16945974	LONP2	cis	parietal	SCAN
rs16945974	LONP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48256400-48256800	Bivalent Enhancer	HepG2	liver

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