Variant report

Variant	rs10496099
Chromosome Location	chr2:62805902-62805903
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	chr2:62805472..62807401-chr2:62822491..62825176,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10172216	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10177638	0.87[EUR][1000 genomes]
rs10186082	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10204410	0.89[AFR][1000 genomes]
rs1038572	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs11125929	0.83[AFR][1000 genomes]
rs11893614	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12328837	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12713462	0.99[AFR][1000 genomes]
rs13423306	0.81[EUR][1000 genomes]
rs1386399	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1406002	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1487074	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs1527959	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1534418	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs1534419	0.92[CEU][hapmap]
rs1534420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1830260	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1843779	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1872789	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs1872790	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs189671	0.86[JPT][hapmap]
rs2129509	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2136737	0.86[JPT][hapmap]
rs2204655	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2204656	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs360799	0.85[JPT][hapmap]
rs360800	0.86[JPT][hapmap]
rs360801	0.86[JPT][hapmap]
rs360804	0.86[JPT][hapmap]
rs360807	0.93[JPT][hapmap]
rs4479415	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671050	0.92[JPT][hapmap]
rs62180020	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6545960	0.84[AFR][1000 genomes]
rs6545961	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6545962	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6545963	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6545965	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545967	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545968	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545969	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs6705835	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6706506	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6727888	0.83[EUR][1000 genomes]
rs6749020	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6752010	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6752597	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6757128	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs7349258	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7573756	0.86[JPT][hapmap]
rs9989741	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3336776	chr2:62747914-62813461	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62798600-62818400	Weak transcription	Esophagus	oesophagus
2	chr2:62801400-62806000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:62802400-62807200	Enhancers	HepG2	liver
4	chr2:62802800-62806600	Enhancers	NHDF-Ad	bronchial
5	chr2:62802800-62807400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:62802800-62807800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:62803000-62806400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:62803400-62807800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:62803800-62807600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:62804000-62806000	Weak transcription	Ovary	ovary
11	chr2:62804400-62806000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:62804400-62808000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:62804600-62806200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:62804600-62806800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:62804600-62807000	Enhancers	HUVEC	blood vessel
16	chr2:62804800-62807000	Enhancers	HSMM	muscle
17	chr2:62804800-62807400	Flanking Active TSS	A549	lung
18	chr2:62805000-62806000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:62805000-62806400	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:62805000-62806600	Enhancers	Adipose Nuclei	Adipose
21	chr2:62805000-62806800	Enhancers	Stomach Mucosa	stomach
22	chr2:62805000-62807000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr2:62805000-62808000	Enhancers	NHLF	lung
24	chr2:62805200-62806000	Enhancers	Brain Anterior Caudate	brain
25	chr2:62805200-62806600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:62805400-62806000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:62805400-62806000	Flanking Active TSS	Hela-S3	cervix
28	chr2:62805400-62806000	Flanking Active TSS	NH-A	brain
29	chr2:62805400-62806600	Enhancers	Pancreas	Pancrea
30	chr2:62805600-62806000	Flanking Active TSS	NHEK	skin
31	chr2:62805600-62806200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:62805800-62806000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr2:62805800-62806200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:62805800-62806200	Flanking Active TSS	HMEC	breast
35	chr2:62805800-62806200	Flanking Active TSS	Osteobl	bone
36	chr2:62805800-62806400	Weak transcription	Small Intestine	intestine
37	chr2:62805800-62807800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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