Variant report

Variant	rs11042601
Chromosome Location	chr11:10077603-10077604
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	chr11:10072187..10074484-chr11:10077289..10078994,2	MCF-7	breast:

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10770103	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840315	1.00[CHB][hapmap]
rs10840325	1.00[CHB][hapmap]
rs10840327	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap]
rs10840330	0.85[CEU][hapmap]
rs10840333	0.85[CEU][hapmap]
rs10840334	0.85[CEU][hapmap]
rs10840337	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840338	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840344	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840359	0.91[EUR][1000 genomes]
rs10840375	0.84[EUR][1000 genomes]
rs10840377	1.00[CEU][hapmap]
rs11042526	1.00[CHB][hapmap]
rs11042543	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap]
rs11042550	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs11042556	1.00[CHB][hapmap]
rs11042559	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs11042561	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs11042571	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042578	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042579	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042580	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11042593	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042615	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11042618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042627	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042632	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042641	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11042686	0.81[GIH][hapmap]
rs11042689	0.81[GIH][hapmap]
rs11600251	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11600489	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11602465	0.80[EUR][1000 genomes]
rs11602515	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs11603440	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606561	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11607582	1.00[CHB][hapmap]
rs11607682	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607703	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360783	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12362060	0.95[CEU][hapmap]
rs12362938	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364676	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417184	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12418212	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418619	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419564	1.00[CHB][hapmap]
rs12419923	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420122	0.83[EUR][1000 genomes]
rs12420734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12420950	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12421179	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421200	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421931	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372807	0.91[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1372808	0.82[EUR][1000 genomes]
rs1442737	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17270804	1.00[CHB][hapmap]
rs17271847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355675	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs17355924	1.00[CHB][hapmap]
rs17356792	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359113	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1822291	0.83[EUR][1000 genomes]
rs1822292	0.95[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs1867135	0.86[EUR][1000 genomes]
rs2197171	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2403227	0.86[CEU][hapmap]
rs2403229	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs2403292	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28731164	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34683105	0.89[EUR][1000 genomes]
rs4271380	0.83[EUR][1000 genomes]
rs4281477	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4385889	0.83[EUR][1000 genomes]
rs4478985	0.88[EUR][1000 genomes]
rs4519084	0.83[EUR][1000 genomes]
rs4529876	0.90[EUR][1000 genomes]
rs4576815	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs4625455	0.91[CEU][hapmap]
rs4643073	0.81[EUR][1000 genomes]
rs4909915	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs4909917	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs4910075	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs4910080	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4910081	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap]
rs4910084	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4910086	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs4910095	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4910098	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55788918	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55796222	0.83[EUR][1000 genomes]
rs56853694	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61877048	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61877049	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878582	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878587	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878622	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878636	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114303	0.91[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs7123453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7123820	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131445	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924875	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7928959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931804	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935774	0.84[EUR][1000 genomes]
rs7935934	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7938491	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7938502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938788	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs7945980	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7946995	0.91[EUR][1000 genomes]
rs7947306	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7948215	0.85[EUR][1000 genomes]
rs7950447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv553476	chr11:10024311-10117435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11042601	OR10A5	cis	cerebellum	SCAN
rs11042601	OR52B2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10066600-10078600	Weak transcription	Aorta	Aorta
2	chr11:10067000-10078400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:10067800-10078200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:10072400-10101200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:10074000-10089200	Weak transcription	Ovary	ovary
6	chr11:10074000-10098200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:10074200-10079200	Weak transcription	Osteobl	bone
8	chr11:10074400-10079200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:10075400-10079000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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