Variant report

Variant	rs11896239
Chromosome Location	chr2:39745999-39746000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10191970	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12475209	1.00[YRI][hapmap]
rs13027520	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13391377	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1526024	0.80[EUR][1000 genomes]
rs17023874	0.83[ASN][1000 genomes]
rs17023923	0.83[ASN][1000 genomes]
rs17532603	0.89[CEU][hapmap]
rs2888602	1.00[JPT][hapmap]
rs35377016	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4670282	0.89[ASN][1000 genomes]
rs4670285	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4670943	0.87[ASN][1000 genomes]
rs56337010	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6740898	0.82[ASN][1000 genomes]
rs72803112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72803115	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs734663	0.92[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7594624	0.83[ASN][1000 genomes]
rs7594967	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9677244	0.81[CEU][hapmap]

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	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39712400-39748600	Weak transcription	Aorta	Aorta
2	chr2:39724800-39750600	Weak transcription	Gastric	stomach
3	chr2:39734600-39746000	Enhancers	Fetal Heart	heart
4	chr2:39741600-39748600	Weak transcription	NHDF-Ad	bronchial
5	chr2:39742800-39746200	Enhancers	Colon Smooth Muscle	Colon
6	chr2:39742800-39746800	Weak transcription	Primary B cells from cord blood	blood
7	chr2:39743000-39747200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:39743000-39750200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:39744000-39748600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:39744200-39747800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:39744200-39748200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:39744200-39748200	Weak transcription	Placenta	Placenta
13	chr2:39744200-39748400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:39744200-39748600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:39744200-39748600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:39744200-39753200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:39744400-39748000	Weak transcription	Fetal Intestine Small	intestine
18	chr2:39744400-39748800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:39744600-39748400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:39744600-39748600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:39744600-39748600	Weak transcription	NHLF	lung
22	chr2:39744800-39748000	Weak transcription	Fetal Intestine Large	intestine
23	chr2:39744800-39748200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:39744800-39748200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:39744800-39748600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:39744800-39748600	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:39744800-39748800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:39744800-39748800	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:39744800-39749800	Weak transcription	Osteobl	bone
30	chr2:39744800-39751200	Weak transcription	Right Ventricle	heart
31	chr2:39745000-39747800	Weak transcription	Fetal Lung	lung
32	chr2:39745000-39748000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:39745000-39748400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:39745000-39748400	Weak transcription	Psoas Muscle	Psoas
35	chr2:39745000-39748600	Weak transcription	Adipose Nuclei	Adipose
36	chr2:39745000-39748600	Weak transcription	Liver	Liver
37	chr2:39745000-39748600	Weak transcription	Left Ventricle	heart
38	chr2:39745000-39749000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:39745000-39749600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:39745000-39749800	Weak transcription	Right Atrium	heart
41	chr2:39745000-39749800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:39745000-39751000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:39745000-39752000	Weak transcription	Brain Angular Gyrus	brain
44	chr2:39745200-39746000	Weak transcription	HSMM	muscle
45	chr2:39745200-39748400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:39745200-39748400	Weak transcription	Fetal Stomach	stomach
47	chr2:39745200-39748800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:39745200-39750200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:39745600-39746200	Transcr. at gene 5' and 3'	HepG2	liver
50	chr2:39745600-39748600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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