Variant report

Variant	rs11892598
Chromosome Location	chr2:72818974-72818975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72357423..72359989-chr2:72817889..72819964,2	MCF-7	breast:
2	chr2:72818726..72821056-chr2:72834950..72837136,2	MCF-7	breast:

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10175824	1.00[ASN][1000 genomes]
rs10176044	1.00[ASN][1000 genomes]
rs10496183	1.00[ASN][1000 genomes]
rs10496184	0.85[CEU][hapmap]
rs10496185	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126367	1.00[ASN][1000 genomes]
rs11126369	0.85[CEU][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs11126378	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs11674508	1.00[ASN][1000 genomes]
rs11675268	0.84[CEU][hapmap]
rs11681845	1.00[ASN][1000 genomes]
rs11684981	1.00[ASN][1000 genomes]
rs11685876	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs11689339	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11689707	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695000	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs11884162	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs11884225	1.00[ASN][1000 genomes]
rs11884266	0.92[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11887356	1.00[ASN][1000 genomes]
rs11897200	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs11903908	1.00[ASN][1000 genomes]
rs1517179	1.00[ASN][1000 genomes]
rs1562361	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17008082	1.00[ASN][1000 genomes]
rs17008143	1.00[ASN][1000 genomes]
rs17008186	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs17008188	1.00[ASN][1000 genomes]
rs17008208	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17008241	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17008293	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008315	0.92[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008360	0.85[CEU][hapmap]
rs17008369	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs17008371	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs17040320	1.00[ASN][1000 genomes]
rs17263172	0.85[CEU][hapmap]
rs1914339	1.00[ASN][1000 genomes]
rs1949377	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs2068410	0.89[YRI][hapmap]
rs2901190	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs34030372	0.81[EUR][1000 genomes]
rs4507127	1.00[ASN][1000 genomes]
rs4508623	1.00[ASN][1000 genomes]
rs4597553	0.89[YRI][hapmap]
rs4852292	0.82[YRI][hapmap]
rs55727931	1.00[ASN][1000 genomes]
rs55728837	1.00[ASN][1000 genomes]
rs55825364	1.00[ASN][1000 genomes]
rs55840408	1.00[ASN][1000 genomes]
rs55939880	1.00[ASN][1000 genomes]
rs56109129	1.00[ASN][1000 genomes]
rs56173504	1.00[ASN][1000 genomes]
rs56184446	1.00[ASN][1000 genomes]
rs56718524	1.00[ASN][1000 genomes]
rs56777837	1.00[ASN][1000 genomes]
rs57192957	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57286048	1.00[ASN][1000 genomes]
rs58033567	1.00[ASN][1000 genomes]
rs58582296	1.00[ASN][1000 genomes]
rs58967293	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59176504	1.00[ASN][1000 genomes]
rs59881252	1.00[ASN][1000 genomes]
rs59974816	1.00[ASN][1000 genomes]
rs60325013	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60536402	1.00[ASN][1000 genomes]
rs60563535	1.00[ASN][1000 genomes]
rs60580301	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60806585	1.00[ASN][1000 genomes]
rs6546769	1.00[ASN][1000 genomes]
rs6546777	0.85[YRI][hapmap]
rs66489235	1.00[ASN][1000 genomes]
rs66539158	1.00[ASN][1000 genomes]
rs66560019	1.00[ASN][1000 genomes]
rs66827358	1.00[ASN][1000 genomes]
rs66920016	1.00[ASN][1000 genomes]
rs67085067	1.00[ASN][1000 genomes]
rs6711442	1.00[ASN][1000 genomes]
rs6711701	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6712930	1.00[ASN][1000 genomes]
rs6712989	1.00[ASN][1000 genomes]
rs6713143	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6713712	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716335	0.96[YRI][hapmap]
rs67166018	1.00[ASN][1000 genomes]
rs6717250	1.00[ASN][1000 genomes]
rs6718052	1.00[ASN][1000 genomes]
rs6720889	0.85[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs6731631	1.00[ASN][1000 genomes]
rs6733532	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs6733538	1.00[ASN][1000 genomes]
rs6735400	1.00[ASN][1000 genomes]
rs6736649	0.80[AFR][1000 genomes]
rs6739768	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6740390	1.00[CEU][hapmap]
rs6743881	1.00[ASN][1000 genomes]
rs6746583	1.00[ASN][1000 genomes]
rs6746586	1.00[ASN][1000 genomes]
rs67491855	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749495	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67535553	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755440	1.00[ASN][1000 genomes]
rs6756070	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6758324	1.00[GIH][hapmap]
rs6758689	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs6761253	0.96[YRI][hapmap]
rs67970313	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72841783	1.00[ASN][1000 genomes]
rs72841795	1.00[ASN][1000 genomes]
rs72845175	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845185	0.86[EUR][1000 genomes]
rs7420583	1.00[ASN][1000 genomes]
rs7424190	1.00[ASN][1000 genomes]
rs7557942	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs7559116	1.00[ASN][1000 genomes]
rs7561471	1.00[ASN][1000 genomes]
rs7565198	0.85[YRI][hapmap]
rs7571483	1.00[ASN][1000 genomes]
rs7571517	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs7573417	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7575050	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs7577244	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7583268	1.00[ASN][1000 genomes]
rs7591025	0.85[YRI][hapmap]
rs7591608	1.00[ASN][1000 genomes]
rs7593084	0.84[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs7596126	1.00[ASN][1000 genomes]
rs7599755	1.00[ASN][1000 genomes]
rs7600134	1.00[ASN][1000 genomes]
rs7603342	1.00[ASN][1000 genomes]
rs7603535	1.00[ASN][1000 genomes]
rs7604083	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7604296	1.00[ASN][1000 genomes]
rs7604818	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs7607226	0.96[YRI][hapmap]
rs7608054	1.00[ASN][1000 genomes]
rs764766	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677947	1.00[ASN][1000 genomes]
rs9678682	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv582208	chr2:72690622-72835886	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv834257	chr2:72701083-72853548	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11892598	AUP1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72804400-72819400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:72809200-72833800	Weak transcription	Left Ventricle	heart
3	chr2:72817800-72821600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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