Variant report

Variant	rs1594503
Chromosome Location	chrX:57480930-57480931
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	chrX:57308677..57309238-chrX:57480174..57481114,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1048358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs1073967	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs10855185	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap]
rs1113635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs1116848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs1160711	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs12393264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs12559310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs12687268	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12688558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12689809	0.85[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap]
rs12689811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1367830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs1431677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs1469592	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1560514	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs1583200	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1586242	0.95[YRI][hapmap]
rs1594506	0.86[YRI][hapmap]
rs1594508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1601317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1601318	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs1835692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1835693	0.91[YRI][hapmap]
rs1835696	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1835698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1864695	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1864697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1997715	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2015312	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs2060113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs2116364	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs2116365	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs2116366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2163537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2195766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2213510	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2217529	0.91[YRI][hapmap]
rs2352862	0.91[YRI][hapmap]
rs2499549	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2499550	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2499555	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs2516019	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2516020	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2516023	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2982252	0.91[YRI][hapmap]
rs2982254	0.91[YRI][hapmap]
rs3015275	0.91[YRI][hapmap]
rs4030473	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4129399	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4319228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4326513	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4557841	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs4587468	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4607761	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4826346	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs4826349	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs4826550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs4826551	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826553	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs4826568	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs5914074	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap]
rs5914084	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs5914085	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs5914095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5914097	0.92[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];0.94[MEX][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap]
rs5914100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5914107	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5914118	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs5914961	0.86[YRI][hapmap]
rs5914962	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs5914980	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs5914993	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs5914994	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs5914999	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap]
rs5915005	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs5915016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5915019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs5915027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs5915047	0.91[YRI][hapmap]
rs5915052	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs5960270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5960951	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap]
rs5960956	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs5960960	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap]
rs5960961	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs5960969	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs5960970	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5960975	0.95[YRI][hapmap]
rs5960980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5961026	0.82[YRI][hapmap]
rs6611612	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6611615	0.87[CHD][hapmap]
rs6611626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs6612796	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs7059676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs717848	0.85[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs7885658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs957721	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs980735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]

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	nsv519013	chrX:57405163-57928734	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1594503	SPIN-2	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:57469000-57481000	Weak transcription	Fetal Intestine Large	intestine
2	chrX:57470200-57486000	Weak transcription	Gastric	stomach
3	chrX:57471000-57481800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chrX:57480000-57481000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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