Variant report

Variant	rs12622447
Chromosome Location	chr2:11475445-11475446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11471245..11477004-chr2:11481417..11486329,8	MCF-7	breast:
2	chr2:11472516..11476992-chr2:11482916..11485822,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10167277	0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap]
rs10187981	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs10192483	0.87[CHB][hapmap]
rs10495582	0.87[CHB][hapmap]
rs10754958	0.87[CHB][hapmap]
rs10929727	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs10929728	1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs11676201	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11680818	0.87[CHB][hapmap]
rs11890858	0.89[ASN][1000 genomes]
rs11890982	0.90[ASN][1000 genomes]
rs11891012	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12463700	0.88[ASN][1000 genomes]
rs12467795	0.87[ASN][1000 genomes]
rs12470004	0.87[CHB][hapmap]
rs12475086	0.87[CHB][hapmap]
rs12478098	0.87[CHB][hapmap]
rs12692436	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12996399	0.91[CHB][hapmap]
rs13018466	0.86[CHB][hapmap]
rs13022598	0.87[CHB][hapmap]
rs13393192	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13397757	0.90[JPT][hapmap]
rs13404430	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs13423864	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13424069	0.86[CHB][hapmap]
rs1515219	0.87[CHB][hapmap]
rs1546597	0.87[CHB][hapmap]
rs1546598	0.87[CHB][hapmap]
rs16857307	0.80[YRI][hapmap]
rs17366643	0.87[CHB][hapmap]
rs17366657	0.86[CHB][hapmap]
rs17463896	0.87[CHB][hapmap]
rs1868585	1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1901010	0.87[CHB][hapmap]
rs2011812	0.87[CHB][hapmap]
rs2056103	0.87[CHB][hapmap]
rs2122383	0.86[CHB][hapmap]
rs2290156	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs34554628	0.82[AFR][1000 genomes]
rs35844125	0.85[AFR][1000 genomes]
rs3732103	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs3771106	0.87[CHB][hapmap]
rs4477886	0.82[CHB][hapmap]
rs4669700	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs4669702	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4669708	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs55859780	0.93[ASN][1000 genomes]
rs6432187	0.81[TSI][hapmap]
rs6705170	0.86[JPT][hapmap]
rs6716447	0.82[CHB][hapmap]
rs6716817	0.81[CHB][hapmap]
rs6728627	0.87[CHB][hapmap]
rs6736194	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6739310	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6743710	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6744083	0.90[ASN][1000 genomes]
rs6753921	0.87[CHB][hapmap]
rs6759032	0.92[ASN][1000 genomes]
rs726843	0.87[CHB][hapmap]
rs7589152	0.87[CHB][hapmap]
rs7589459	0.90[ASN][1000 genomes]
rs7598032	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs7605784	0.90[ASN][1000 genomes]
rs7605793	0.93[ASN][1000 genomes]
rs8996	0.87[CHB][hapmap]
rs978906	0.87[CHB][hapmap]
rs9798189	0.82[AMR][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	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11457200-11476400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:11461000-11476400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:11467000-11480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:11467400-11481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:11467600-11481600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:11467800-11480200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:11468000-11476400	Weak transcription	Psoas Muscle	Psoas
8	chr2:11468400-11481200	Weak transcription	HUVEC	blood vessel
9	chr2:11470400-11479800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:11470400-11481400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:11470800-11475800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:11470800-11481200	Weak transcription	Right Atrium	heart
13	chr2:11470800-11481800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:11471000-11481200	Weak transcription	HSMM	muscle
15	chr2:11471200-11478600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:11471200-11480400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:11471400-11475800	Enhancers	Liver	Liver
18	chr2:11471600-11477000	Enhancers	HepG2	liver
19	chr2:11472200-11476400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:11472200-11476400	Weak transcription	Pancreas	Pancrea
21	chr2:11472200-11482800	Weak transcription	Gastric	stomach
22	chr2:11473200-11475600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:11473200-11476200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:11473600-11479800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:11473800-11479600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:11474000-11477000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:11474000-11479800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:11474200-11476400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:11474200-11480000	Weak transcription	Adipose Nuclei	Adipose
30	chr2:11474800-11476000	Enhancers	A549	lung
31	chr2:11475000-11476000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:11475000-11481200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:11475200-11475600	Weak transcription	Stomach Mucosa	stomach
34	chr2:11475200-11475600	Enhancers	NH-A	brain
35	chr2:11475200-11476000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr2:11475200-11476000	Enhancers	NHDF-Ad	bronchial
37	chr2:11475200-11476000	Enhancers	Osteobl	bone
38	chr2:11475200-11476200	Enhancers	Hela-S3	cervix
39	chr2:11475400-11475600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr2:11475400-11475800	Enhancers	NHLF	lung
41	chr2:11475400-11476000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr2:11475400-11476400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:11475400-11479800	Weak transcription	Aorta	Aorta
44	chr2:11475400-11481000	Weak transcription	Ovary	ovary

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