Variant report

Variant	rs3212428
Chromosome Location	chr5:52325314-52325315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10940289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12109479	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2233213	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2233216	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2233220	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212534	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212538	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212541	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212602	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212608	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212639	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816326	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3928414	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41308283	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7732191	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968673	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:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52307000-52333800	Weak transcription	Gastric	stomach
2	chr5:52314200-52328600	Weak transcription	Lung	lung
3	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:52314400-52326200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:52317200-52327200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:52317400-52326800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:52317600-52326800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:52317600-52333600	Weak transcription	Colonic Mucosa	Colon
9	chr5:52318400-52331800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:52318800-52327200	Genic enhancers	HMEC	breast
11	chr5:52319000-52325400	Enhancers	Brain Substantia Nigra	brain
12	chr5:52319200-52325400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:52319200-52326200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:52319200-52327600	Weak transcription	Fetal Intestine Large	intestine
15	chr5:52319600-52326600	Weak transcription	Small Intestine	intestine
16	chr5:52320600-52326200	Weak transcription	Esophagus	oesophagus
17	chr5:52320600-52327400	Weak transcription	HSMM	muscle
18	chr5:52320600-52327600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:52321000-52326600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:52321600-52326800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:52321800-52326000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:52321800-52326800	Weak transcription	Fetal Lung	lung
23	chr5:52322200-52326400	Genic enhancers	HepG2	liver
24	chr5:52322200-52333200	Weak transcription	Fetal Stomach	stomach
25	chr5:52322600-52326400	Weak transcription	Fetal Kidney	kidney
26	chr5:52323000-52326400	Genic enhancers	Hela-S3	cervix
27	chr5:52323000-52327000	Enhancers	A549	lung
28	chr5:52323000-52327200	Genic enhancers	NHEK	skin
29	chr5:52323200-52326400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:52323200-52326400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:52323200-52327000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:52323200-52329000	Enhancers	NHLF	lung
33	chr5:52323400-52325800	Enhancers	Osteobl	bone
34	chr5:52323600-52326200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:52323600-52326200	Enhancers	NHDF-Ad	bronchial
36	chr5:52323600-52332600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:52323800-52326200	Weak transcription	Pancreas	Pancrea
38	chr5:52324200-52326600	Weak transcription	Stomach Mucosa	stomach
39	chr5:52324200-52334200	Weak transcription	Spleen	Spleen
40	chr5:52324400-52326400	Weak transcription	Dnd41	blood
41	chr5:52324400-52326800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:52324400-52327000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:52324400-52327200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:52324400-52327400	Weak transcription	Brain Angular Gyrus	brain
45	chr5:52324400-52328800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
47	chr5:52324600-52326800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:52324600-52327000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:52324600-52332400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:52324800-52325800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links