Variant report

Variant	rs13401937
Chromosome Location	chr2:55252214-55252215
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55245011..55247166-chr2:55250682..55252602,2	MCF-7	breast:
2	chr2:55243166..55246645-chr2:55249862..55254918,6	K562	blood:
3	chr2:55251702..55254676-chr2:55343936..55346646,2	K562	blood:
4	chr2:55241211..55243006-chr2:55251751..55254579,2	K562	blood:
5	chr2:55251918..55254652-chr2:55395890..55398049,2	K562	blood:
6	chr2:55251258..55253325-chr2:55261770..55263673,2	K562	blood:
7	chr2:55238125..55242197-chr2:55249599..55253048,4	K562	blood:
8	chr2:55238547..55240641-chr2:55252176..55254092,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10084445	0.82[AFR][1000 genomes]
rs10170102	0.89[AFR][1000 genomes]
rs10179491	0.99[AFR][1000 genomes]
rs10180207	0.87[AFR][1000 genomes]
rs10181115	0.89[AFR][1000 genomes]
rs10191684	0.88[AFR][1000 genomes]
rs10198096	0.85[AFR][1000 genomes]
rs11125554	0.82[AFR][1000 genomes]
rs13394823	0.82[AFR][1000 genomes]
rs13394824	0.82[AFR][1000 genomes]
rs17046567	0.84[AFR][1000 genomes]
rs17046569	0.84[AFR][1000 genomes]
rs3925500	1.00[ASN][1000 genomes]
rs4444576	0.81[EUR][1000 genomes]
rs58482670	1.00[ASN][1000 genomes]
rs58499715	1.00[ASN][1000 genomes]
rs61621549	1.00[ASN][1000 genomes]
rs73936513	1.00[ASN][1000 genomes]
rs73936813	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 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	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55237600-55258600	Weak transcription	Ovary	ovary
3	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
4	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
5	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
7	chr2:55241400-55253400	Weak transcription	Fetal Lung	lung
8	chr2:55242000-55252400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:55242200-55253400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:55242400-55253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:55242400-55258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:55243000-55262400	Weak transcription	Hela-S3	cervix
13	chr2:55243200-55252600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:55243800-55259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:55245000-55256000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:55245400-55253400	Weak transcription	Liver	Liver
17	chr2:55245600-55265600	Weak transcription	Stomach Mucosa	stomach
18	chr2:55246400-55254000	Enhancers	Brain Substantia Nigra	brain
19	chr2:55246800-55259800	Weak transcription	NH-A	brain
20	chr2:55248200-55253200	Weak transcription	Fetal Intestine Large	intestine
21	chr2:55248200-55253600	Weak transcription	Fetal Intestine Small	intestine
22	chr2:55248200-55253800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:55248200-55255200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:55248200-55255200	Weak transcription	Left Ventricle	heart
25	chr2:55248200-55258400	Weak transcription	Lung	lung
26	chr2:55248200-55259200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:55248600-55256400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:55249000-55256200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:55249000-55256600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:55249000-55256600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr2:55249000-55256600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr2:55249000-55256600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:55249200-55255000	Strong transcription	Dnd41	blood
34	chr2:55249200-55256600	Enhancers	Brain Angular Gyrus	brain
35	chr2:55249400-55253000	Enhancers	NHLF	lung
36	chr2:55249400-55253600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:55249400-55254000	Genic enhancers	HSMM	muscle
38	chr2:55249400-55254800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:55249400-55254800	Genic enhancers	Brain Anterior Caudate	brain
40	chr2:55249400-55255200	Weak transcription	Brain Germinal Matrix	brain
41	chr2:55249400-55256400	Enhancers	Adipose Nuclei	Adipose
42	chr2:55249600-55254400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:55249800-55253000	Weak transcription	NHEK	skin
44	chr2:55249800-55255200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr2:55249800-55255200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:55249800-55255800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr2:55250000-55252400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:55250000-55253600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:55250000-55256000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:55250000-55256400	Enhancers	Colon Smooth Muscle	Colon

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