Variant report

Variant	rs11895352
Chromosome Location	chr2:20367135-20367136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20362106..20364188-chr2:20366369..20369040,2	MCF-7	breast:
2	chr2:20364675..20367244-chr2:20367416..20369596,2	K562	blood:
3	chr2:20366533..20369508-chr2:20380029..20382114,2	MCF-7	breast:
4	chr2:20364027..20368295-chr2:20377113..20381748,5	MCF-7	breast:
5	chr2:20364604..20368497-chr2:20376297..20379611,4	MCF-7	breast:
6	chr2:20366147..20368368-chr2:20415586..20417297,2	MCF-7	breast:
7	chr2:20365445..20367731-chr2:20374746..20377053,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266059	Chromatin interaction
ENSG00000200763	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1107850	0.83[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1107851	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1107852	0.81[CHB][hapmap]
rs11096641	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11693335	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11899121	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478327	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13009332	0.89[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs13010903	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1473886	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2090032	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2090034	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35135293	0.89[ASN][1000 genomes]
rs6531216	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6728072	0.89[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs7577335	0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs870526	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs870527	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907866	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907867	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907868	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1005923	chr2:20344028-20369781	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv997958	chr2:20349343-20386339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv999131	chr2:20350751-20377607	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv998067	chr2:20350751-20386339	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv3446690	chr2:20362971-20367169	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv3451715	chr2:20363271-20367769	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv3364595	chr2:20363371-20367169	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20362400-20371400	Weak transcription	Right Atrium	heart
2	chr2:20363800-20374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:20364000-20367800	Enhancers	A549	lung
4	chr2:20364000-20368000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:20364200-20368000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:20364200-20369200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:20364400-20367400	Enhancers	GM12878-XiMat	blood
8	chr2:20364400-20367400	Enhancers	NHDF-Ad	bronchial
9	chr2:20364400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:20364600-20367600	Enhancers	HMEC	breast
11	chr2:20364800-20372200	Enhancers	NHEK	skin
12	chr2:20365000-20368400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:20365000-20368600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:20365200-20367200	Enhancers	NHLF	lung
15	chr2:20365200-20367400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:20365200-20367600	Enhancers	NH-A	brain
17	chr2:20365600-20367400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:20365600-20367400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:20365600-20367400	Enhancers	Osteobl	bone
20	chr2:20365600-20367800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:20365800-20367200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:20365800-20367200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr2:20365800-20367400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:20365800-20367400	Enhancers	HSMM	muscle
25	chr2:20365800-20367600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:20365800-20367600	Enhancers	Pancreas	Pancrea
27	chr2:20365800-20367800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:20365800-20368400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr2:20365800-20369800	Weak transcription	Lung	lung
30	chr2:20366000-20367200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:20366000-20367400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:20366000-20367400	Enhancers	HSMMtube	muscle
33	chr2:20366000-20367600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:20366000-20367600	Enhancers	Esophagus	oesophagus
35	chr2:20366000-20369600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr2:20366000-20370400	Weak transcription	Fetal Kidney	kidney
37	chr2:20366000-20370800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:20366000-20371200	Weak transcription	Fetal Lung	lung
39	chr2:20366200-20367200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:20366200-20369000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:20366400-20367400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:20366400-20367800	Bivalent Enhancer	HepG2	liver
43	chr2:20366400-20369200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:20366400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:20366600-20367200	Enhancers	Stomach Mucosa	stomach
46	chr2:20366600-20367800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:20366600-20369200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:20366600-20369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:20366600-20371600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:20366800-20367600	Enhancers	Fetal Heart	heart

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