Variant report

Variant	rs11739898
Chromosome Location	chr5:179401490-179401491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10051694	0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap]
rs10056991	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap]
rs10071652	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11249664	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11249665	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11750102	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap]
rs17681274	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2278662	0.86[JPT][hapmap]
rs4700852	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4700864	0.83[JPT][hapmap]
rs62404970	0.86[AFR][1000 genomes]
rs6601077	0.87[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap]
rs6862105	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap]
rs6869349	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6873317	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6873639	1.00[JPT][hapmap]
rs6884565	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6898203	0.86[JPT][hapmap]
rs7734329	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9329095	1.00[JPT][hapmap];0.82[YRI][hapmap]

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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11739898	RASGEF1C	cis	cerebellum	SCAN
rs11739898	C5orf45	cis	parietal	SCAN
rs11739898	GRM6	cis	cerebellum	SCAN
rs11739898	CLTB	cis	parietal	SCAN
rs11739898	PROP1	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179373800-179401600	Weak transcription	Colonic Mucosa	Colon
2	chr5:179376600-179406600	Weak transcription	Psoas Muscle	Psoas
3	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
4	chr5:179381000-179407800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:179381200-179402200	Weak transcription	Fetal Heart	heart
6	chr5:179381200-179405600	Weak transcription	NHLF	lung
7	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:179381800-179402200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:179383200-179408600	Weak transcription	A549	lung
10	chr5:179388600-179404000	Weak transcription	HMEC	breast
11	chr5:179388800-179405000	Weak transcription	HUVEC	blood vessel
12	chr5:179388800-179405800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:179389000-179405800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr5:179389200-179403400	Weak transcription	Hela-S3	cervix
15	chr5:179389400-179411400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:179391200-179403800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:179391800-179406200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:179392400-179402000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:179392600-179414800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:179393200-179404000	Weak transcription	NH-A	brain
21	chr5:179393600-179403400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:179394400-179405200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:179395000-179403000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:179395000-179405600	Weak transcription	Stomach Mucosa	stomach
25	chr5:179395200-179401800	Weak transcription	HepG2	liver
26	chr5:179396600-179403200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:179396600-179404200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:179396600-179461800	Weak transcription	HSMM	muscle
29	chr5:179396800-179401800	Weak transcription	HSMMtube	muscle
30	chr5:179398400-179402800	Weak transcription	Primary T cells from cord blood	blood
31	chr5:179399000-179401600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr5:179399000-179406800	Strong transcription	Fetal Muscle Leg	muscle
33	chr5:179399000-179408000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:179399000-179408400	Strong transcription	Brain Germinal Matrix	brain
35	chr5:179399200-179405200	Strong transcription	Pancreas	Pancrea
36	chr5:179399200-179405800	Strong transcription	Adipose Nuclei	Adipose
37	chr5:179399200-179406800	Strong transcription	Fetal Stomach	stomach
38	chr5:179399400-179405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:179399400-179408000	Strong transcription	Left Ventricle	heart
40	chr5:179399400-179408200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:179399800-179408400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:179400000-179402400	Strong transcription	Liver	Liver
43	chr5:179400000-179405000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:179400000-179405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:179400000-179408400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:179400000-179411400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr5:179400200-179401600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:179400200-179401600	Strong transcription	Spleen	Spleen
49	chr5:179400200-179402000	Strong transcription	Fetal Kidney	kidney
50	chr5:179400200-179402200	Strong transcription	Fetal Lung	lung

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