Variant report

Variant	rs11187952
Chromosome Location	chr10:96206104-96206105
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96205685..96208642-chr10:96211882..96213579,2	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10786168	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10786169	1.00[CEU][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes]
rs1079504	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10882452	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882454	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10882460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882469	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10882470	0.95[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10882471	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10882473	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10882474	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs10882477	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11187937	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187938	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11187939	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187940	0.92[JPT][hapmap]
rs11187944	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187948	0.84[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11187958	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11187960	1.00[JPT][hapmap]
rs11187966	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11187972	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11187973	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11187980	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11187985	0.86[AMR][1000 genomes]
rs11187996	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11188009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11188012	0.83[JPT][hapmap];0.80[YRI][hapmap]
rs11188019	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs11188020	1.00[JPT][hapmap]
rs11188040	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11527881	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11592354	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11638	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12218213	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12218216	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12219906	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12220588	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12221475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12572040	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12762574	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1326839	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs1334595	1.00[JPT][hapmap]
rs1359263	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1749352	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1749355	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1749356	0.81[EUR][1000 genomes]
rs1886272	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1889485	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1889486	0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1931757	0.83[JPT][hapmap]
rs1969815	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1977288	1.00[JPT][hapmap]
rs1977291	0.83[JPT][hapmap]
rs1980741	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2095380	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2244241	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2265362	0.82[EUR][1000 genomes]
rs2265364	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274096	0.82[EUR][1000 genomes]
rs2274417	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2281791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2860760	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2860821	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2901764	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2901765	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3740358	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs3758523	0.80[EUR][1000 genomes]
rs3781262	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4316436	0.82[AMR][1000 genomes]
rs4351744	1.00[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4611135	0.82[EUR][1000 genomes]
rs480032	1.00[JPT][hapmap]
rs4917505	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4918333	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4918402	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs4918404	0.83[EUR][1000 genomes]
rs4918409	0.85[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4918419	0.85[CEU][hapmap]
rs493088	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs517784	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522111	0.82[EUR][1000 genomes]
rs541704	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs542540	0.81[EUR][1000 genomes]
rs555782	0.81[EUR][1000 genomes]
rs556055	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56020662	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs576517	0.81[EUR][1000 genomes]
rs581165	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6583942	1.00[JPT][hapmap]
rs6583943	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6583944	0.85[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs6583946	0.80[EUR][1000 genomes]
rs692872	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs701885	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs7073639	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078236	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7078478	0.83[JPT][hapmap]
rs7078811	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap]
rs7079934	0.83[EUR][1000 genomes]
rs7083898	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7086462	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7087472	0.81[AMR][1000 genomes]
rs7087798	0.83[JPT][hapmap]
rs7089094	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7092129	1.00[JPT][hapmap]
rs7393251	0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7895305	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7898330	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7906843	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs7913343	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7921721	1.00[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8181426	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs912466	0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9420641	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs945123	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs955694	0.83[EUR][1000 genomes]
rs9633675	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9633699	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11187952	KIF11	cis	cerebellum	SCAN
rs11187952	HELLS	cis	cerebellum	SCAN
rs11187952	FGFBP3	cis	cerebellum	SCAN
rs11187952	C19orf22	trans	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96188400-96213600	Weak transcription	Stomach Mucosa	stomach
2	chr10:96190800-96234600	Weak transcription	Osteobl	bone
3	chr10:96192000-96211400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:96198400-96218200	Weak transcription	Aorta	Aorta
5	chr10:96199200-96211200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr10:96199200-96215400	Weak transcription	Fetal Stomach	stomach
7	chr10:96199400-96207000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:96199400-96211200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:96199400-96211400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:96199400-96211400	Weak transcription	Psoas Muscle	Psoas
11	chr10:96199400-96212000	Weak transcription	Adipose Nuclei	Adipose
12	chr10:96199400-96215200	Weak transcription	Placenta	Placenta
13	chr10:96199400-96219600	Weak transcription	Pancreas	Pancrea
14	chr10:96200200-96211400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:96200200-96219400	Weak transcription	Left Ventricle	heart
16	chr10:96200600-96211200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:96201200-96219200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:96202400-96210000	Weak transcription	Fetal Lung	lung
19	chr10:96203000-96218600	Weak transcription	Ovary	ovary
20	chr10:96203000-96239600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr10:96203200-96215400	Weak transcription	Fetal Intestine Small	intestine
22	chr10:96203400-96212000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:96203400-96242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:96203600-96206600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:96203600-96211400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr10:96203600-96218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:96203800-96211200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr10:96203800-96211200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:96203800-96211400	Weak transcription	Brain Substantia Nigra	brain
30	chr10:96203800-96217200	Weak transcription	HepG2	liver
31	chr10:96203800-96219600	Weak transcription	Brain Angular Gyrus	brain
32	chr10:96204000-96221000	Weak transcription	Liver	Liver
33	chr10:96204200-96210400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr10:96204200-96211200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:96204200-96212000	Weak transcription	Brain Anterior Caudate	brain
36	chr10:96204200-96213400	Weak transcription	A549	lung
37	chr10:96204200-96243400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr10:96205800-96206200	Strong transcription	HSMM	muscle

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