Variant report

Variant	rs13410228
Chromosome Location	chr2:58372594-58372595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10165760	0.82[AFR][1000 genomes]
rs10182762	0.83[AFR][1000 genomes]
rs10184957	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11883874	0.82[AFR][1000 genomes]
rs11891477	0.83[AFR][1000 genomes]
rs11903212	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12104650	0.82[AFR][1000 genomes]
rs12616896	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12624152	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713376	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12988249	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13006005	0.91[EUR][1000 genomes]
rs13023405	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13032851	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13405281	0.82[AFR][1000 genomes]
rs13410500	0.82[AFR][1000 genomes]
rs13422760	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1371213	0.93[AFR][1000 genomes]
rs1404457	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1404459	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1404460	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2312486	0.94[AFR][1000 genomes]
rs34335951	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34556232	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35773188	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35925771	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755296	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3771222	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55809167	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57112138	0.88[AFR][1000 genomes]
rs57267169	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58470176	0.82[AFR][1000 genomes]
rs61746304	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6709533	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6714952	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752935	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs716758	0.93[AFR][1000 genomes]
rs72951048	0.82[AFR][1000 genomes]
rs72951056	0.82[AFR][1000 genomes]
rs7558066	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7561771	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7569731	0.81[AFR][1000 genomes]
rs9973928	0.84[AFR][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	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
2	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:58340600-58373600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:58344400-58386000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:58346000-58384400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:58346600-58373600	Weak transcription	NHEK	skin
8	chr2:58346800-58387200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:58347200-58373800	Weak transcription	Hela-S3	cervix
10	chr2:58347800-58384000	Weak transcription	Fetal Kidney	kidney
11	chr2:58347800-58386600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:58348400-58373400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:58348400-58373600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:58348600-58382400	Weak transcription	Fetal Intestine Large	intestine
15	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:58350400-58383800	Weak transcription	K562	blood
17	chr2:58351000-58382400	Weak transcription	Esophagus	oesophagus
18	chr2:58351000-58384600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:58353800-58388200	Weak transcription	Small Intestine	intestine
20	chr2:58358200-58393800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:58358400-58389000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:58358800-58382400	Weak transcription	Pancreas	Pancrea
23	chr2:58358800-58385200	Weak transcription	Placenta	Placenta
24	chr2:58358800-58385600	Weak transcription	Fetal Thymus	thymus
25	chr2:58359000-58386600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:58359000-58387400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:58359000-58391400	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:58359200-58373400	Weak transcription	HMEC	breast
31	chr2:58359200-58381800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:58359200-58382400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:58359200-58382400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:58359200-58384400	Weak transcription	Left Ventricle	heart
35	chr2:58359200-58395200	Weak transcription	Fetal Stomach	stomach
36	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:58359400-58385600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:58359400-58389400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:58359600-58385600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:58359800-58384400	Weak transcription	HepG2	liver
41	chr2:58359800-58392000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:58360800-58385000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:58360800-58388600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:58361000-58373800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:58361200-58373400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:58361400-58373600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:58363600-58384600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:58365000-58373800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links