Variant report

Variant	rs11904139
Chromosome Location	chr2:40511165-40511166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1990608	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2110744	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2160237	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952402	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544315	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6544316	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6544317	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6544318	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6748881	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs998260	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3343138	chr2:40510648-40512796	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40500200-40514600	Weak transcription	Fetal Brain Male	brain
2	chr2:40503600-40514800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr2:40506400-40516800	Weak transcription	Small Intestine	intestine
4	chr2:40506600-40514600	Weak transcription	Brain Germinal Matrix	brain
5	chr2:40506800-40517200	Weak transcription	Dnd41	blood
6	chr2:40507600-40511200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:40508000-40511400	Flanking Active TSS	HSMMtube	muscle
8	chr2:40508000-40517200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:40508600-40511400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:40509000-40514800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:40509000-40519400	Weak transcription	Fetal Stomach	stomach
12	chr2:40509200-40512600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:40509200-40517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:40509400-40511200	Active TSS	Ovary	ovary
15	chr2:40509600-40511200	Enhancers	Left Ventricle	heart
16	chr2:40510000-40511200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:40510000-40511400	Enhancers	Colon Smooth Muscle	Colon
18	chr2:40510000-40512000	Weak transcription	Psoas Muscle	Psoas
19	chr2:40510000-40513600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:40510200-40511200	Enhancers	Rectal Smooth Muscle	rectum
21	chr2:40510200-40511200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr2:40510200-40512800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:40510200-40513800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:40510200-40514000	Weak transcription	NH-A	brain
25	chr2:40510200-40514200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:40510200-40514800	Weak transcription	Right Atrium	heart
27	chr2:40510400-40511200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:40510400-40511400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr2:40510600-40511200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:40510600-40511200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:40510600-40511200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:40510600-40512000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:40510600-40514800	Genic enhancers	Fetal Heart	heart
34	chr2:40510800-40511200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:40510800-40511200	Genic enhancers	Monocytes-CD14+_RO01746	blood
36	chr2:40510800-40511400	Enhancers	Brain Cingulate Gyrus	brain
37	chr2:40510800-40512000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:40510800-40512800	Enhancers	HSMM	muscle
39	chr2:40510800-40513800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:40511000-40511200	Enhancers	Brain Angular Gyrus	brain
41	chr2:40511000-40511400	Enhancers	Brain Anterior Caudate	brain
42	chr2:40511000-40512000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:40511000-40512000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:40511000-40512000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:40511000-40512000	Weak transcription	NHDF-Ad	bronchial
46	chr2:40511000-40512000	Weak transcription	Osteobl	bone
47	chr2:40511000-40512200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:40511000-40512200	Weak transcription	Brain Substantia Nigra	brain
49	chr2:40511000-40512400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:40511000-40513800	Weak transcription	NHEK	skin

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