Variant report

Variant	rs57742023
Chromosome Location	chr3:53226997-53226998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53219801..53222487-chr3:53226191..53228055,3	K562	blood:
2	chr3:53220786..53223807-chr3:53225456..53227755,4	K562	blood:
3	chr3:53192673..53196741-chr3:53226099..53230036,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12490555	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490645	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2230494	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306572	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306574	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773722	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs45596236	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62254320	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53197600-53227600	Weak transcription	Hela-S3	cervix
2	chr3:53200600-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:53201600-53228000	Weak transcription	NH-A	brain
4	chr3:53202000-53228400	Weak transcription	Fetal Kidney	kidney
5	chr3:53202800-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:53203600-53229800	Weak transcription	A549	lung
7	chr3:53205600-53229800	Weak transcription	Brain Angular Gyrus	brain
8	chr3:53206800-53228000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:53207200-53227400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:53207200-53227600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:53209600-53228000	Weak transcription	HUVEC	blood vessel
12	chr3:53209600-53228400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:53210000-53229000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:53210600-53228400	Strong transcription	Gastric	stomach
15	chr3:53211000-53227400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:53211400-53227800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:53211800-53227800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:53212200-53227000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:53214200-53229600	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:53214400-53229600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:53214800-53228800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:53214800-53229600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:53214800-53229800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:53215000-53229800	Weak transcription	Fetal Brain Female	brain
25	chr3:53215400-53228800	Strong transcription	Placenta	Placenta
26	chr3:53216000-53227800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:53216000-53229800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:53216200-53229800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:53217200-53227800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:53217400-53227000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:53217800-53227400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:53217800-53229600	Weak transcription	Brain Anterior Caudate	brain
33	chr3:53217800-53229800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:53219400-53229800	Weak transcription	K562	blood
35	chr3:53219800-53227400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:53220000-53230600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:53220600-53227800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:53221600-53227000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:53221600-53228000	Weak transcription	HSMM	muscle
40	chr3:53222000-53228400	Weak transcription	HSMMtube	muscle
41	chr3:53222400-53227000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:53222400-53227200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:53222800-53227400	Strong transcription	Colonic Mucosa	Colon
44	chr3:53223000-53227400	Strong transcription	Fetal Intestine Large	intestine
45	chr3:53223200-53228200	Weak transcription	Osteobl	bone
46	chr3:53223200-53229200	Strong transcription	Fetal Intestine Small	intestine
47	chr3:53223800-53229000	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr3:53224000-53227800	Weak transcription	Small Intestine	intestine
49	chr3:53224000-53229800	Weak transcription	Brain Germinal Matrix	brain
50	chr3:53224200-53227000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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