Variant report

Variant	rs2345874
Chromosome Location	chr2:153251476-153251477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10931079	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11696004	1.00[JPT][hapmap]
rs12476186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693362	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13010632	0.81[MEX][hapmap]
rs13388095	1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs16831021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[ASN][1000 genomes]
rs16831065	1.00[CHB][hapmap];0.90[MEX][hapmap];0.83[ASN][1000 genomes]
rs16831082	0.92[ASN][1000 genomes]
rs16831093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16831100	0.93[ASN][1000 genomes]
rs16831118	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2345811	0.82[JPT][hapmap]
rs2345894	0.82[JPT][hapmap]
rs2346203	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2881335	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34006820	0.84[ASN][1000 genomes]
rs35662043	0.90[ASN][1000 genomes]
rs3811576	1.00[JPT][hapmap]
rs4254462	0.82[JPT][hapmap]
rs4664558	0.82[JPT][hapmap]
rs66663920	0.96[ASN][1000 genomes]
rs6746538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751576	0.81[MEX][hapmap]
rs6757782	1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs6761178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67689907	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67761838	0.92[ASN][1000 genomes]
rs73012774	0.92[ASN][1000 genomes]
rs73012784	0.92[ASN][1000 genomes]
rs7587450	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7601047	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153226200-153251800	Weak transcription	HSMMtube	muscle
2	chr2:153229200-153252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:153233800-153255400	Weak transcription	NHEK	skin
4	chr2:153237400-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:153237400-153255400	Weak transcription	HMEC	breast
6	chr2:153238600-153258600	Weak transcription	Left Ventricle	heart
7	chr2:153241200-153251600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:153241200-153255400	Weak transcription	Pancreas	Pancrea
9	chr2:153242800-153252600	Weak transcription	A549	lung
10	chr2:153243000-153251600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:153243400-153252600	Weak transcription	Fetal Brain Female	brain
12	chr2:153243800-153252000	Weak transcription	Fetal Lung	lung
13	chr2:153245000-153251800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:153246400-153251600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:153246600-153266600	Enhancers	Brain Substantia Nigra	brain
16	chr2:153247000-153251800	Enhancers	Brain Anterior Caudate	brain
17	chr2:153247000-153257800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:153247200-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:153247400-153251600	Weak transcription	Ovary	ovary
20	chr2:153247400-153252600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:153247400-153252600	Weak transcription	Fetal Stomach	stomach
22	chr2:153247400-153255400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:153247400-153277600	Weak transcription	Fetal Intestine Small	intestine
24	chr2:153247800-153258800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:153248200-153251600	Weak transcription	Psoas Muscle	Psoas
26	chr2:153248200-153251800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:153248800-153253600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:153249000-153252400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:153249000-153252600	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:153249200-153252600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr2:153249200-153253800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr2:153249200-153254200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:153249400-153251600	Weak transcription	Aorta	Aorta
34	chr2:153249400-153253200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:153249600-153251600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:153249600-153255400	Weak transcription	Gastric	stomach
37	chr2:153249600-153255400	Weak transcription	Lung	lung
38	chr2:153249600-153259000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:153249800-153251600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:153250000-153252000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr2:153250000-153252400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:153250000-153253200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:153250000-153254200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr2:153250200-153251600	Enhancers	Adipose Nuclei	Adipose
45	chr2:153250200-153252600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:153250400-153251600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:153250400-153257600	Weak transcription	HepG2	liver
48	chr2:153250600-153252400	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:153250600-153252600	Enhancers	Brain Hippocampus Middle	brain
50	chr2:153250800-153251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links