Variant report

Variant	rs3980393
Chromosome Location	chr11:36234049-36234050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11033500	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs11033501	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs11033503	0.83[ASN][1000 genomes]
rs11033504	0.83[ASN][1000 genomes]
rs11600365	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs11601619	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs11602141	0.85[CHB][hapmap]
rs11602754	0.87[ASN][1000 genomes]
rs11605931	0.87[ASN][1000 genomes]
rs12420852	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs12421151	0.93[CHB][hapmap];0.96[ASN][1000 genomes]
rs12421199	0.85[CHB][hapmap]
rs12421400	0.87[ASN][1000 genomes]
rs12574172	0.85[ASN][1000 genomes]
rs12574419	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs12574525	0.87[ASN][1000 genomes]
rs12575304	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs12575540	0.85[ASN][1000 genomes]
rs12575617	0.87[ASN][1000 genomes]
rs12575645	0.87[ASN][1000 genomes]
rs12577437	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs1374376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405095	0.83[CHB][hapmap]
rs16928506	0.87[ASN][1000 genomes]
rs16928509	0.87[ASN][1000 genomes]
rs16928510	0.87[ASN][1000 genomes]
rs16928513	0.87[ASN][1000 genomes]
rs16928514	0.88[ASN][1000 genomes]
rs16928552	0.85[CHB][hapmap]
rs34892666	0.87[ASN][1000 genomes]
rs3812769	0.87[ASN][1000 genomes]
rs3812771	0.87[ASN][1000 genomes]
rs3812772	0.87[ASN][1000 genomes]
rs4417242	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs4417243	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs4468324	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs4485080	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs4611176	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs4755440	0.84[CEU][hapmap]
rs4755443	0.85[AFR][1000 genomes]
rs58048041	0.85[ASN][1000 genomes]
rs58648806	0.83[ASN][1000 genomes]
rs58707777	0.85[ASN][1000 genomes]
rs59051429	0.85[ASN][1000 genomes]
rs59137935	0.85[ASN][1000 genomes]
rs60544801	0.83[ASN][1000 genomes]
rs60759289	0.85[ASN][1000 genomes]
rs61254236	0.85[ASN][1000 genomes]
rs61879013	0.86[ASN][1000 genomes]
rs61879034	0.87[ASN][1000 genomes]
rs61879035	0.87[ASN][1000 genomes]
rs61879036	0.87[ASN][1000 genomes]
rs61879037	0.91[ASN][1000 genomes]
rs61881463	0.87[ASN][1000 genomes]
rs61881464	0.87[ASN][1000 genomes]
rs61881465	0.85[ASN][1000 genomes]
rs61881468	0.85[ASN][1000 genomes]
rs61881469	0.85[ASN][1000 genomes]
rs61881470	0.85[ASN][1000 genomes]
rs61881476	0.85[ASN][1000 genomes]
rs6416084	0.81[CEU][hapmap]
rs6484828	1.00[YRI][hapmap]
rs7110064	0.83[ASN][1000 genomes]
rs72937449	0.87[ASN][1000 genomes]
rs72937454	0.88[ASN][1000 genomes]
rs72937494	0.91[ASN][1000 genomes]
rs72941791	0.85[ASN][1000 genomes]
rs7931368	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7946514	0.85[AFR][1000 genomes]
rs872534	0.85[CHB][hapmap]
rs940923	0.85[CHB][hapmap]

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	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv897225	chr11:36136912-36244190	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36218000-36252200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:36219200-36248600	Weak transcription	Ovary	ovary
3	chr11:36220600-36241600	Weak transcription	HSMM	muscle
4	chr11:36221400-36235200	Weak transcription	Fetal Intestine Small	intestine
5	chr11:36221400-36248800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:36222000-36239800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:36222200-36234600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:36222200-36235000	Weak transcription	Esophagus	oesophagus
9	chr11:36222800-36248800	Weak transcription	HSMMtube	muscle
10	chr11:36226800-36241600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:36227000-36238400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:36229400-36236600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:36231400-36237800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr11:36231600-36234200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:36231600-36237200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:36232200-36241400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:36232400-36234600	Enhancers	Fetal Brain Female	brain
18	chr11:36232800-36234600	Enhancers	Fetal Kidney	kidney
19	chr11:36232800-36235000	Weak transcription	NHEK	skin
20	chr11:36232800-36235200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:36232800-36235200	Weak transcription	HMEC	breast
22	chr11:36232800-36235800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:36232800-36235800	Enhancers	Fetal Lung	lung
24	chr11:36232800-36237200	Enhancers	Brain Hippocampus Middle	brain
25	chr11:36232800-36237800	Enhancers	Brain Substantia Nigra	brain
26	chr11:36233000-36234200	Enhancers	Brain Germinal Matrix	brain
27	chr11:36233000-36234400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr11:36233000-36235200	Enhancers	Fetal Muscle Leg	muscle
29	chr11:36233000-36235800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:36233000-36236000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:36233000-36236200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:36233000-36237200	Enhancers	Fetal Brain Male	brain
33	chr11:36233000-36237600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr11:36233200-36235200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:36233200-36237600	Enhancers	Brain Anterior Caudate	brain
36	chr11:36233400-36234400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr11:36233400-36234800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:36233400-36235000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr11:36233400-36235400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:36233400-36235400	Enhancers	Brain Angular Gyrus	brain
41	chr11:36233400-36237800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:36233800-36234200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:36233800-36234400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr11:36233800-36235000	Enhancers	Fetal Stomach	stomach
45	chr11:36233800-36237800	Enhancers	Placenta Amnion	Placenta Amnion
46	chr11:36234000-36234200	Enhancers	Fetal Intestine Large	intestine
47	chr11:36234000-36235000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr11:36234000-36244600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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