Variant report

Variant	rs2233220
Chromosome Location	chr5:52394626-52394627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52392231..52395065-chr5:52398498..52400912,2	K562	blood:
2	chr5:52384559..52387537-chr5:52393582..52396762,3	MCF-7	breast:
3	chr5:52391585..52394108-chr5:52394132..52397970,3	K562	blood:

Variant related genes	Relation type
ENSG00000272123	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10940289	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12109479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2233213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212427	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212428	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212437	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212454	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212460	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212462	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212477	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212534	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212538	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212541	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212602	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212608	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212639	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3928414	0.86[EUR][1000 genomes]
rs41308283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7732191	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9968622	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9968673	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:52341200-52396400	Strong transcription	HMEC	breast
3	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
5	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
7	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
8	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
9	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:52372200-52394800	Weak transcription	Gastric	stomach
11	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
12	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:52382800-52395000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:52383000-52394800	Weak transcription	Brain Anterior Caudate	brain
16	chr5:52383200-52394800	Weak transcription	Esophagus	oesophagus
17	chr5:52383200-52394800	Weak transcription	Spleen	Spleen
18	chr5:52383800-52395000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:52384000-52394800	Weak transcription	Brain Substantia Nigra	brain
20	chr5:52384000-52395200	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:52384200-52394800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:52385800-52395800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr5:52386200-52394800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:52386400-52394800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:52386400-52394800	Weak transcription	GM12878-XiMat	blood
26	chr5:52386600-52394800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:52387400-52394800	Weak transcription	Fetal Brain Male	brain
28	chr5:52387600-52394800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:52387600-52405000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:52388000-52394800	Weak transcription	Ovary	ovary
31	chr5:52388000-52395000	Weak transcription	Lung	lung
32	chr5:52388200-52398400	Strong transcription	HUVEC	blood vessel
33	chr5:52388400-52396200	Weak transcription	Hela-S3	cervix
34	chr5:52389400-52404800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr5:52389600-52395000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:52389800-52394800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:52390000-52397600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:52390200-52403800	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:52390600-52396200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:52390600-52397200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:52390600-52399600	Strong transcription	NHEK	skin
42	chr5:52390600-52401200	Strong transcription	Dnd41	blood
43	chr5:52390800-52394800	Weak transcription	Primary B cells from cord blood	blood
44	chr5:52390800-52396400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr5:52390800-52403800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:52391000-52395600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:52391000-52401000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr5:52391000-52403000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:52391400-52395000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:52391600-52403200	Weak transcription	Fetal Heart	heart

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