Variant report

Variant	rs3212627
Chromosome Location	chr5:52380923-52380924
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52285755..52287338-chr5:52380121..52382244,2	MCF-7	breast:
2	chr5:52372832..52374615-chr5:52379311..52380988,2	K562	blood:
3	chr5:52380023..52382035-chr5:52385112..52387338,2	K562	blood:

Variant related genes	Relation type
ENSG00000272123	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10042752	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10065796	1.00[JPT][hapmap]
rs10071255	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10073544	1.00[JPT][hapmap]
rs12523395	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1421941	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs16880636	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3212386	0.86[YRI][hapmap]
rs3212574	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3212621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58786195	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6883028	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7722066	0.86[YRI][hapmap]
rs9292002	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9292003	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv880598	chr5:52379277-52382904	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:52341200-52396400	Strong transcription	HMEC	breast
5	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:52342600-52383800	Strong transcription	NHEK	skin
7	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
8	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
10	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
11	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
14	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
16	chr5:52362200-52387800	Strong transcription	HepG2	liver
17	chr5:52362400-52382400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:52363400-52382600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
20	chr5:52366000-52382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
22	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:52367600-52381200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr5:52367600-52385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:52367800-52386000	Strong transcription	NH-A	brain
26	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
27	chr5:52369000-52381000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:52369400-52382600	Weak transcription	Brain Angular Gyrus	brain
30	chr5:52369400-52383600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
33	chr5:52372000-52382600	Weak transcription	Brain Anterior Caudate	brain
34	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
35	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:52372200-52382600	Weak transcription	Lung	lung
37	chr5:52372200-52382800	Weak transcription	Spleen	Spleen
38	chr5:52372200-52384800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:52372200-52394800	Weak transcription	Gastric	stomach
41	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
42	chr5:52372400-52385000	Weak transcription	Osteobl	bone
43	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr5:52372800-52386400	Weak transcription	NHDF-Ad	bronchial
45	chr5:52373000-52385600	Weak transcription	Ovary	ovary
46	chr5:52373000-52387000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:52373400-52382600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:52373800-52386200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:52374200-52382600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:52374200-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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