Variant report

Variant	rs3212640
Chromosome Location	chr5:52383718-52383719
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52382323..52385100-chr5:52387808..52389930,2	K562	blood:
2	chr5:52376435..52379263-chr5:52381516..52385182,3	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1062535	0.89[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs1126643	0.89[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12515364	0.88[ASN][1000 genomes]
rs12517446	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12518279	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12521915	0.89[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs12652168	0.84[ASN][1000 genomes]
rs1421929	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1421930	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1421931	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1421932	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1833558	0.83[ASN][1000 genomes]
rs1862191	0.83[ASN][1000 genomes]
rs1991013	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2075615	0.83[ASN][1000 genomes]
rs2075616	0.93[ASN][1000 genomes]
rs2075617	0.92[ASN][1000 genomes]
rs2287871	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303122	0.89[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2303123	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2303127	0.84[ASN][1000 genomes]
rs2897458	0.83[ASN][1000 genomes]
rs2910964	0.83[ASN][1000 genomes]
rs2910965	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910971	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2974976	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2974978	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2974987	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212467	0.88[ASN][1000 genomes]
rs3212472	0.87[ASN][1000 genomes]
rs3212508	0.83[ASN][1000 genomes]
rs3212509	0.83[ASN][1000 genomes]
rs3212522	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212527	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212533	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212591	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212600	0.84[ASN][1000 genomes]
rs3212601	0.83[ASN][1000 genomes]
rs3212619	0.86[ASN][1000 genomes]
rs67719154	0.84[ASN][1000 genomes]
rs6898333	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7725246	0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs984966	0.84[ASN][1000 genomes]
rs989073	0.87[ASN][1000 genomes]
rs990602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv880346	chr5:52381216-52385312	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 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	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
18	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
19	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:52367600-52385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:52367800-52386000	Strong transcription	NH-A	brain
22	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
23	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
26	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
27	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:52372200-52384800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:52372200-52394800	Weak transcription	Gastric	stomach
31	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
32	chr5:52372400-52385000	Weak transcription	Osteobl	bone
33	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:52372800-52386400	Weak transcription	NHDF-Ad	bronchial
35	chr5:52373000-52385600	Weak transcription	Ovary	ovary
36	chr5:52373000-52387000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:52373800-52386200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:52374200-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:52375800-52384000	Strong transcription	NHLF	lung
40	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:52379200-52388400	Strong transcription	Hela-S3	cervix
42	chr5:52380000-52391200	Weak transcription	Fetal Brain Female	brain
43	chr5:52381000-52384600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:52381000-52384600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr5:52381000-52384800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr5:52381000-52385200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:52381000-52386200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:52381200-52385000	Weak transcription	Primary T cells from cord blood	blood
49	chr5:52381200-52385000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:52381200-52385000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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