Variant report

Variant	rs12417184
Chromosome Location	chr11:10136860-10136861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10136561..10138179-chr11:10323345..10325457,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254554	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10743129	0.82[EUR][1000 genomes]
rs10770103	0.83[EUR][1000 genomes]
rs10840327	0.94[CEU][hapmap]
rs10840337	0.80[EUR][1000 genomes]
rs10840338	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840344	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10840359	0.89[EUR][1000 genomes]
rs10840375	0.84[EUR][1000 genomes]
rs10840377	0.89[CEU][hapmap]
rs11042543	0.94[CEU][hapmap]
rs11042561	0.94[CEU][hapmap]
rs11042571	0.81[EUR][1000 genomes]
rs11042578	0.80[EUR][1000 genomes]
rs11042579	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs11042593	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11042595	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11042601	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042609	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042615	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042618	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11042623	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042627	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11042632	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042641	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042683	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11600251	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11600489	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11602515	0.83[CEU][hapmap]
rs11603440	0.80[EUR][1000 genomes]
rs11606561	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11607682	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11607703	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12360783	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12362060	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs12362938	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12364676	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12418212	0.82[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12418619	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12419923	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12420122	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12420734	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12420950	0.84[EUR][1000 genomes]
rs12421096	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12421179	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12421200	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs12421931	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13306112	1.00[YRI][hapmap]
rs13306113	1.00[YRI][hapmap]
rs1372807	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs1372808	0.81[EUR][1000 genomes]
rs1372811	1.00[CHB][hapmap]
rs1442737	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1470258	1.00[YRI][hapmap]
rs17271847	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs17356792	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs17359113	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1822290	0.82[YRI][hapmap]
rs1822291	0.83[EUR][1000 genomes]
rs1822292	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1822293	1.00[CHB][hapmap]
rs1867135	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2044146	0.82[YRI][hapmap]
rs2083712	0.82[YRI][hapmap]
rs2083713	0.82[YRI][hapmap]
rs2197171	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2403229	0.88[CEU][hapmap]
rs2403292	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28731164	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920154	0.82[YRI][hapmap]
rs34683105	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4271380	0.82[EUR][1000 genomes]
rs4281477	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4385889	0.83[EUR][1000 genomes]
rs4478985	0.89[EUR][1000 genomes]
rs4519084	0.83[EUR][1000 genomes]
rs4529876	0.90[EUR][1000 genomes]
rs4576815	0.88[CEU][hapmap]
rs4625455	0.83[CEU][hapmap]
rs4643073	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4909915	0.83[CEU][hapmap]
rs4909917	0.88[CEU][hapmap]
rs4910081	0.94[CEU][hapmap]
rs4910086	0.88[CEU][hapmap]
rs4910093	0.82[YRI][hapmap]
rs4910095	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4910098	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4910111	1.00[CHB][hapmap]
rs55788918	0.83[EUR][1000 genomes]
rs55796222	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56853694	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61877048	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61877049	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61878582	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61878587	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61878622	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61878636	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7110151	1.00[CHB][hapmap]
rs7114303	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs7123453	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7123820	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7124401	1.00[CHB][hapmap]
rs7131445	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7924875	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7928959	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7931804	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7935774	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7935934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7938491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7938502	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7938647	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7938788	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs7945980	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7946995	0.88[EUR][1000 genomes]
rs7947306	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948215	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7950447	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][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	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
2	nsv1039636	chr11:10126747-10280570	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1036041	chr11:10131018-10212202	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10120400-10142800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr11:10122200-10144200	Weak transcription	Left Ventricle	heart
3	chr11:10122200-10156400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:10122400-10138600	Weak transcription	Esophagus	oesophagus
5	chr11:10122800-10141200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:10122800-10142600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:10123200-10156400	Weak transcription	Fetal Intestine Small	intestine
8	chr11:10126200-10143000	Weak transcription	Ovary	ovary
9	chr11:10131200-10144200	Weak transcription	Psoas Muscle	Psoas
10	chr11:10131400-10139200	Weak transcription	HUVEC	blood vessel
11	chr11:10131400-10142800	Weak transcription	Fetal Brain Male	brain
12	chr11:10131600-10139200	Weak transcription	HSMMtube	muscle
13	chr11:10131600-10139600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:10131800-10139000	Weak transcription	Fetal Lung	lung
15	chr11:10131800-10139000	Weak transcription	HSMM	muscle
16	chr11:10131800-10143600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:10132200-10143000	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:10135400-10137000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:10135400-10139600	Enhancers	NHDF-Ad	bronchial
20	chr11:10135600-10137200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:10136000-10137000	Enhancers	Adipose Nuclei	Adipose
22	chr11:10136000-10137200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:10136000-10137200	Enhancers	NHLF	lung
24	chr11:10136200-10137200	Enhancers	A549	lung
25	chr11:10136200-10137200	Enhancers	Osteobl	bone
26	chr11:10136400-10137000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:10136400-10137200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:10136600-10137000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:10136600-10138400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:10136600-10139000	Weak transcription	Hela-S3	cervix
31	chr11:10136800-10139000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:10136800-10143000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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