Variant report

Variant	rs12523395
Chromosome Location	chr5:52334774-52334775
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	chr5:52326404..52328383-chr5:52333260..52335027,2	MCF-7	breast:
2	chr5:52285122..52287993-chr5:52333837..52337640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164171	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10042752	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs10065796	1.00[JPT][hapmap]
rs10071255	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10073544	1.00[JPT][hapmap]
rs12514668	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1421941	0.90[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs16880636	0.90[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[AFR][1000 genomes]
rs1862639	0.89[CHD][hapmap];0.81[GIH][hapmap]
rs3212386	1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap]
rs3212412	0.84[AMR][1000 genomes]
rs3212417	0.88[CEU][hapmap]
rs3212574	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3212621	1.00[ASN][1000 genomes]
rs3212627	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs58786195	0.87[ASN][1000 genomes]
rs66789666	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67217308	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67835512	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6883028	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7722066	0.87[YRI][hapmap]
rs9292002	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9292003	1.00[JPT][hapmap]

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	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv881217	chr5:52334774-52341512	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv881071	chr5:52334774-52362765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:52328600-52335200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:52328800-52335800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
8	chr5:52329400-52335600	Weak transcription	Dnd41	blood
9	chr5:52331000-52336200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:52331000-52337000	Weak transcription	Fetal Kidney	kidney
11	chr5:52331800-52334800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:52331800-52334800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:52331800-52335200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:52331800-52337200	Enhancers	HUVEC	blood vessel
15	chr5:52332000-52334800	Enhancers	Brain Hippocampus Middle	brain
16	chr5:52332800-52334800	Enhancers	Stomach Mucosa	stomach
17	chr5:52333000-52334800	Enhancers	Brain Substantia Nigra	brain
18	chr5:52333400-52337000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:52333400-52341400	Strong transcription	HepG2	liver
20	chr5:52333600-52336800	Weak transcription	Fetal Lung	lung
21	chr5:52333800-52334800	Enhancers	Left Ventricle	heart
22	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
24	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
26	chr5:52334200-52334800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:52334200-52334800	Enhancers	Esophagus	oesophagus
28	chr5:52334200-52334800	Enhancers	Right Atrium	heart
29	chr5:52334200-52334800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr5:52334200-52337000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:52334400-52334800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:52334400-52334800	Enhancers	Pancreas	Pancrea
33	chr5:52334400-52335600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:52334400-52336200	Enhancers	HMEC	breast
35	chr5:52334400-52337000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:52334400-52338000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:52334600-52335000	Genic enhancers	NHEK	skin
39	chr5:52334600-52336000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:52334600-52336400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:52334600-52336400	Enhancers	Hela-S3	cervix
42	chr5:52334600-52337000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr5:52334600-52337000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr5:52334600-52337000	Weak transcription	A549	lung
45	chr5:52334600-52337000	Weak transcription	NH-A	brain
46	chr5:52334600-52337000	Weak transcription	NHDF-Ad	bronchial
47	chr5:52334600-52337000	Weak transcription	NHLF	lung
48	chr5:52334600-52337000	Weak transcription	Osteobl	bone
49	chr5:52334600-52337400	Weak transcription	Adipose Nuclei	Adipose
50	chr5:52334600-52343400	Weak transcription	Gastric	stomach

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