Variant report

Variant	rs966045
Chromosome Location	chr4:21848082-21848083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR125-2	chr4:21844963-21854811	UM9-5
2	lnc-GPR125-2	chr4:21844964-21854811	NONHSAT095745
3	lnc-GPR125-2	chr4:21846984-21849319	NONHSAT095746

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10006785	0.87[EUR][1000 genomes]
rs10012747	0.83[CHB][hapmap]
rs10016234	0.87[EUR][1000 genomes]
rs10031539	0.83[CHB][hapmap]
rs10033249	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10034603	0.82[CHB][hapmap]
rs1040036	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs10516402	0.92[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10938858	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11942219	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11944786	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12498561	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12503736	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12504827	0.85[CEU][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs12512316	0.85[CEU][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs12513218	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12642007	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12642061	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12642992	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12643557	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12643656	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12644852	0.83[EUR][1000 genomes]
rs12646630	0.83[CHB][hapmap]
rs12649356	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12650029	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12650691	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1349383	0.89[CEU][hapmap]
rs1349384	0.83[CHB][hapmap]
rs1380270	0.83[CHB][hapmap]
rs1398833	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1398834	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459274	0.83[CHB][hapmap]
rs1459277	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1459278	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1459281	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1562815	0.83[CHB][hapmap]
rs168625	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17498679	0.83[CHB][hapmap]
rs17498715	0.86[CHB][hapmap]
rs1809267	0.83[CHB][hapmap]
rs1813583	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1827591	0.89[CEU][hapmap];0.83[CHB][hapmap];0.93[TSI][hapmap]
rs1839523	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1841185	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1841186	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1968778	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap]
rs2007970	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs2007971	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2012445	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2018175	0.83[CHB][hapmap]
rs2044804	0.83[EUR][1000 genomes]
rs2044805	0.83[EUR][1000 genomes]
rs2063656	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs2063657	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs2063658	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs2122592	0.82[CHB][hapmap]
rs28409267	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33939152	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34226435	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34384769	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34580494	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34825575	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34833395	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34903275	0.83[EUR][1000 genomes]
rs35609084	0.83[CHB][hapmap]
rs360687	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360688	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360700	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4282162	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap]
rs4377576	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4411977	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4563486	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55777248	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6448069	0.82[CHB][hapmap]
rs6448072	0.83[CHB][hapmap]
rs6448075	0.85[CHB][hapmap]
rs6840539	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6856781	0.82[CHB][hapmap]
rs73256549	0.83[EUR][1000 genomes]
rs73256551	0.83[EUR][1000 genomes]
rs73256552	0.83[EUR][1000 genomes]
rs73256555	0.83[EUR][1000 genomes]
rs73256556	0.83[EUR][1000 genomes]
rs73256557	0.83[EUR][1000 genomes]
rs73256558	0.83[EUR][1000 genomes]
rs73256559	0.83[EUR][1000 genomes]
rs73256561	0.83[EUR][1000 genomes]
rs73256572	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73256581	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73256595	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73256601	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73258503	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7375384	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs7378252	0.83[CHB][hapmap]
rs7664617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs9291430	0.82[CHB][hapmap]
rs9760244	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9884923	0.83[CHB][hapmap]
rs9994945	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817467	chr4:21602921-22422816	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs966045	QDPR	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21840800-21849600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:21846600-21848200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:21847800-21849600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:21848000-21848200	Enhancers	Ovary	ovary
5	chr4:21848000-21849000	Weak transcription	Osteobl	bone
6	chr4:21848000-21849200	Weak transcription	Muscle Satellite Cultured Cells	--

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