Variant report

Variant	rs717531
Chromosome Location	chr4:21764761-21764762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:21513582..21515656-chr4:21764630..21766290,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10011983	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs10012055	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10017454	0.88[EUR][1000 genomes]
rs10017728	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs10028109	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10028154	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10030629	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10034770	0.90[CHB][hapmap]
rs10805229	0.90[CHB][hapmap]
rs11732235	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11930660	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11930835	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11935715	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11939687	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11942569	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12501226	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12509958	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12513185	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12513386	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13107513	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13107915	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs13109215	0.90[CHB][hapmap]
rs13122692	0.85[CHB][hapmap]
rs13122849	0.90[CHB][hapmap]
rs13138025	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1380269	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1450729	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1450730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs1450731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1459270	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1459271	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1459272	0.80[EUR][1000 genomes]
rs1459273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1471222	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1513572	0.85[CHB][hapmap]
rs1530816	0.87[CHB][hapmap]
rs1824366	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1824367	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1827592	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1839525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1841179	0.80[ASN][1000 genomes]
rs1841180	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1841181	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1841183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841184	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1847425	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1868742	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1868743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1868744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017960	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2045555	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs2175783	0.90[CHB][hapmap]
rs2323160	0.81[CHB][hapmap]
rs2874961	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34105626	0.80[EUR][1000 genomes]
rs34322864	0.84[EUR][1000 genomes]
rs3864177	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4101629	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4361375	0.80[ASN][1000 genomes]
rs4495027	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4496573	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4530617	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs4550912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs4568228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4697241	0.86[CHB][hapmap]
rs4697244	0.81[CHB][hapmap]
rs5011097	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5011098	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55877532	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6414727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6448074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6448077	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448078	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448080	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448082	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448083	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448085	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448098	0.81[CHB][hapmap]
rs6822291	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6838654	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs6838747	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6845965	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6852732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855072	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715840	0.90[CHB][hapmap]
rs7376538	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7658944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668222	0.85[CHB][hapmap]
rs7681415	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7696243	0.90[CHB][hapmap]
rs7697475	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[ASN][1000 genomes]
rs868745	0.81[CHB][hapmap]
rs896122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966922	0.86[CHB][hapmap]
rs987045	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv878751	chr4:21712050-21793807	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv4269	chr4:21761429-21806056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs717531	QDPR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21762000-21765800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr4:21764000-21766000	Enhancers	Colon Smooth Muscle	Colon
3	chr4:21764200-21766400	Enhancers	Fetal Heart	heart
4	chr4:21764600-21765000	Enhancers	HMEC	breast
5	chr4:21764600-21765200	Enhancers	Fetal Brain Female	brain
6	chr4:21764600-21765600	Enhancers	Rectal Smooth Muscle	rectum

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