Variant report

Variant	rs10734652
Chromosome Location	chr11:10150212-10150213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10128601	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10500722	0.86[YRI][hapmap]
rs10500724	0.86[YRI][hapmap]
rs10770080	0.81[JPT][hapmap]
rs10770082	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10770083	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10770084	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10770087	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10770088	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10770089	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10770090	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10770106	0.89[CEU][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs10840332	0.80[ASW][hapmap]
rs10840346	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840349	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840353	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840354	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840357	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840358	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840360	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840363	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840364	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs10840365	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840368	0.86[ASN][1000 genomes]
rs10840369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042602	0.89[EUR][1000 genomes]
rs11042617	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042620	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042621	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042622	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042625	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042633	0.85[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs11042638	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042702	0.82[YRI][hapmap]
rs11042717	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs11600852	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12224149	0.91[ASN][1000 genomes]
rs12288355	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12360854	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1442738	0.90[JPT][hapmap];0.93[YRI][hapmap]
rs2403230	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2403259	0.81[JPT][hapmap]
rs2403264	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs2403265	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2403290	0.91[EUR][1000 genomes]
rs4284389	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4316505	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4323860	0.82[YRI][hapmap]
rs4350354	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4366476	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4444073	0.92[CEU][hapmap]
rs4466825	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4509749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4597056	0.86[YRI][hapmap]
rs4635071	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910097	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4910107	0.80[JPT][hapmap];0.93[YRI][hapmap]
rs4910115	0.86[YRI][hapmap]
rs58623593	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6483883	0.93[ASW][hapmap]
rs6483964	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6483965	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6483966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6483970	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6484147	0.81[ASW][hapmap];0.86[YRI][hapmap]
rs6484152	0.86[YRI][hapmap]
rs7102016	0.93[ASW][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs7104821	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7106328	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7106491	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7107021	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7107290	0.85[YRI][hapmap]
rs7110312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110664	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7111072	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7115944	0.89[JPT][hapmap];0.96[YRI][hapmap]
rs7119000	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7121704	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7122422	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs7123728	0.82[YRI][hapmap]
rs7125593	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7126376	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs7128591	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7128698	0.93[ASW][hapmap]
rs7131203	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs726102	0.82[YRI][hapmap]
rs7479039	0.88[YRI][hapmap]
rs7924499	0.86[ASN][1000 genomes]
rs7928170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7932988	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938543	0.86[YRI][hapmap]
rs7938891	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7939146	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7942420	0.86[ASN][1000 genomes]
rs7947588	0.83[ASN][1000 genomes]
rs7947666	0.86[YRI][hapmap]
rs7948166	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7950140	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7950240	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9645625	0.85[CEU][hapmap];0.87[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10734652	SYT9	cis	cerebellum	SCAN
rs10734652	ZNF143	cis	cerebellum	SCAN
rs10734652	RP11-351I24.1	cis	Whole Blood	GTEx
rs10734652	OR52B2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10122200-10156400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:10123200-10156400	Weak transcription	Fetal Intestine Small	intestine
3	chr11:10137200-10161800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:10140000-10156200	Weak transcription	Fetal Lung	lung
5	chr11:10144200-10160800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:10144400-10152600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:10144600-10156400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:10144800-10152600	Weak transcription	Ovary	ovary
9	chr11:10144800-10154800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:10144800-10155200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:10144800-10161400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:10144800-10161400	Weak transcription	HSMM	muscle
13	chr11:10144800-10170400	Weak transcription	Left Ventricle	heart
14	chr11:10145400-10160800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:10145400-10160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:10145800-10156400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:10147800-10160800	Weak transcription	NHEK	skin
18	chr11:10148000-10161000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:10148200-10160800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:10148400-10160800	Weak transcription	Adipose Nuclei	Adipose
21	chr11:10148400-10161400	Weak transcription	NHLF	lung
22	chr11:10148600-10160800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:10148800-10160800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:10149200-10150400	Weak transcription	NHDF-Ad	bronchial
25	chr11:10149200-10154200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:10149200-10162800	Weak transcription	Monocytes-CD14+_RO01746	blood

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