Variant report

Variant	rs10840369
Chromosome Location	chr11:10136428-10136429
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	chr11:10129087..10131222-chr11:10133484..10136579,3	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10128601	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10500722	0.86[YRI][hapmap]
rs10500724	0.84[YRI][hapmap]
rs10734652	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]
rs10770082	1.00[CEU][hapmap];0.96[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10770083	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10770084	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10770087	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10770088	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10770089	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10770090	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10770096	0.82[ASN][1000 genomes]
rs10770106	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs10840346	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10840349	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840353	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840354	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840357	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840358	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840360	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840363	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840364	1.00[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs10840365	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840368	0.91[ASN][1000 genomes]
rs11042582	0.80[CHB][hapmap]
rs11042602	0.88[EUR][1000 genomes]
rs11042617	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042620	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11042621	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042622	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042625	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042633	0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs11042638	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042702	0.82[YRI][hapmap]
rs11042717	0.92[CEU][hapmap]
rs11600852	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12224149	0.85[ASN][1000 genomes]
rs12288355	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12360854	1.00[CEU][hapmap];0.96[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1442738	0.86[JPT][hapmap];0.93[YRI][hapmap]
rs2403230	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2403264	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[EUR][1000 genomes]
rs2403265	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2403290	0.90[EUR][1000 genomes]
rs4284389	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4316505	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4323860	0.82[YRI][hapmap]
rs4350354	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4366476	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4444073	0.92[CEU][hapmap]
rs4466825	1.00[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4509749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4597056	0.86[YRI][hapmap]
rs4635071	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4910097	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4910107	0.93[YRI][hapmap]
rs4910115	0.84[YRI][hapmap]
rs58623593	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6483964	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6483965	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6483966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6483970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6484147	0.86[YRI][hapmap]
rs6484152	0.84[YRI][hapmap]
rs7102016	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs7104821	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7106328	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7106491	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7107021	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7107290	0.84[YRI][hapmap]
rs7110312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7110664	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7111072	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7115944	0.86[JPT][hapmap];0.96[YRI][hapmap]
rs7119000	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7121704	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7122422	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7123728	0.81[YRI][hapmap]
rs7125593	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7126376	1.00[CEU][hapmap];0.96[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7128591	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7131203	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs726102	0.82[YRI][hapmap]
rs7479039	0.86[YRI][hapmap]
rs7924499	0.81[ASN][1000 genomes]
rs7928170	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs7932988	1.00[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7938543	0.84[YRI][hapmap]
rs7938891	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7939146	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7942420	0.81[ASN][1000 genomes]
rs7947666	0.84[YRI][hapmap]
rs7948166	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7950140	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7950240	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9645625	0.86[CEU][hapmap];0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10840369	RP11-351I24.1	cis	Whole Blood	GTEx

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	chr11:10135800-10136600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:10136000-10137000	Enhancers	Adipose Nuclei	Adipose
23	chr11:10136000-10137200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:10136000-10137200	Enhancers	NHLF	lung
25	chr11:10136200-10137200	Enhancers	A549	lung
26	chr11:10136200-10137200	Enhancers	Osteobl	bone
27	chr11:10136400-10136600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:10136400-10136600	Enhancers	Hela-S3	cervix
29	chr11:10136400-10136800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr11:10136400-10136800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:10136400-10137000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:10136400-10137200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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