Variant report

Variant	rs3212619
Chromosome Location	chr5:52378295-52378296
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	chr5:52372459..52375173-chr5:52375877..52379453,3	MCF-7	breast:
2	chr5:52376435..52379263-chr5:52381516..52385182,3	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1062535	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1126643	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12515364	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12517446	0.80[ASN][1000 genomes]
rs12518279	0.85[ASN][1000 genomes]
rs12521915	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12652168	0.86[ASN][1000 genomes]
rs1421929	0.85[ASN][1000 genomes]
rs1421930	0.85[ASN][1000 genomes]
rs1421931	0.85[ASN][1000 genomes]
rs1421932	0.85[ASN][1000 genomes]
rs1833558	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1862191	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1991013	0.86[ASN][1000 genomes]
rs2075615	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075616	0.83[ASN][1000 genomes]
rs2075617	0.82[ASN][1000 genomes]
rs2287871	0.85[ASN][1000 genomes]
rs2303122	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303123	0.94[ASN][1000 genomes]
rs2303127	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2897458	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910964	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910965	0.85[ASN][1000 genomes]
rs2910971	0.85[ASN][1000 genomes]
rs2974976	0.85[ASN][1000 genomes]
rs2974978	0.85[ASN][1000 genomes]
rs2974987	0.85[ASN][1000 genomes]
rs3212467	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3212472	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212508	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212509	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212522	0.85[ASN][1000 genomes]
rs3212527	0.85[ASN][1000 genomes]
rs3212533	0.85[ASN][1000 genomes]
rs3212591	0.85[ASN][1000 genomes]
rs3212600	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3212601	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212640	0.86[ASN][1000 genomes]
rs67719154	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6880055	0.80[EUR][1000 genomes]
rs6898333	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7725246	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs984966	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989073	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs990602	0.86[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	nsv880866	chr5:52358262-52378295	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:75 , 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	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
3	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:52341200-52396400	Strong transcription	HMEC	breast
6	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:52342600-52383800	Strong transcription	NHEK	skin
8	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
9	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
11	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
12	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:52349400-52379600	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:52352400-52379200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
17	chr5:52359400-52380000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
20	chr5:52362200-52387800	Strong transcription	HepG2	liver
21	chr5:52362400-52382400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:52363400-52382600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
24	chr5:52366000-52382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
26	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:52367600-52381200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr5:52367600-52385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:52367800-52386000	Strong transcription	NH-A	brain
30	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
31	chr5:52369000-52381000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:52369400-52382600	Weak transcription	Brain Angular Gyrus	brain
34	chr5:52369400-52383600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:52369800-52379800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
38	chr5:52372000-52382600	Weak transcription	Brain Anterior Caudate	brain
39	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
40	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr5:52372200-52382600	Weak transcription	Lung	lung
42	chr5:52372200-52382800	Weak transcription	Spleen	Spleen
43	chr5:52372200-52384800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:52372200-52394800	Weak transcription	Gastric	stomach
46	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
47	chr5:52372400-52385000	Weak transcription	Osteobl	bone
48	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr5:52372800-52386400	Weak transcription	NHDF-Ad	bronchial
50	chr5:52373000-52385600	Weak transcription	Ovary	ovary

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