Variant report

Variant	rs11709788
Chromosome Location	chr3:49349444-49349445
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr3:49348501-49349476	GM12878	blood:	n/a	n/a
2	RUNX3	chr3:49348527-49349472	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
USP4	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11707940	0.90[ASN][1000 genomes]
rs11720964	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11920251	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493284	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12497569	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12715435	0.88[ASN][1000 genomes]
rs13077723	0.93[ASN][1000 genomes]
rs13078949	0.95[ASN][1000 genomes]
rs1865741	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2230929	0.88[ASN][1000 genomes]
rs34142492	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34366700	0.85[ASN][1000 genomes]
rs34514189	0.83[ASN][1000 genomes]
rs34567776	0.88[ASN][1000 genomes]
rs34915642	0.98[ASN][1000 genomes]
rs35446411	0.90[ASN][1000 genomes]
rs35869135	0.93[ASN][1000 genomes]
rs3774799	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4554002	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955431	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56038006	0.90[ASN][1000 genomes]
rs67882627	0.90[ASN][1000 genomes]
rs6795772	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73086105	0.90[ASN][1000 genomes]
rs7374375	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7640903	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9818758	0.85[ASN][1000 genomes]
rs9863142	0.95[ASN][1000 genomes]
rs9864406	0.98[ASN][1000 genomes]
rs9873994	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11709788	WDR6	cis	Esophagus Mucosa	GTEx
rs11709788	WDR6	cis	lung	GTEx
rs11709788	WDR6	cis	Nerve Tibial	GTEx
rs11709788	AMT	cis	Muscle Skeletal	GTEx
rs11709788	WDR6	cis	Adipose Subcutaneous	GTEx
rs11709788	WDR6	cis	Muscle Skeletal	GTEx
rs11709788	WDR6	cis	Artery Tibial	GTEx
rs11709788	NCKIPSD	cis	Muscle Skeletal	GTEx
rs11709788	AMT	cis	Thyroid	GTEx
rs11709788	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11709788	WDR6	cis	Whole Blood	GTEx
rs11709788	PH-4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49314800-49355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:49315200-49349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:49315200-49349600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:49315200-49352600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
9	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
10	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
12	chr3:49317400-49349600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:49319400-49349600	Strong transcription	Liver	Liver
17	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:49320000-49349600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:49320200-49375000	Strong transcription	Thymus	Thymus
20	chr3:49320600-49351400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:49320800-49368000	Strong transcription	Primary T cells from cord blood	blood
22	chr3:49321800-49373600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:49326800-49373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:49326800-49375000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:49332400-49351400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:49332600-49354400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:49333600-49369600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr3:49335000-49351000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:49335000-49365200	Strong transcription	Spleen	Spleen
30	chr3:49335000-49369400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:49335000-49375000	Strong transcription	Placenta	Placenta
32	chr3:49335200-49349800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:49335200-49351200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:49335200-49351400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:49335200-49365200	Strong transcription	Lung	lung
36	chr3:49335200-49369800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr3:49335200-49375200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:49335400-49365200	Strong transcription	Fetal Muscle Leg	muscle
39	chr3:49335800-49351600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:49336200-49351000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:49336200-49354200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:49336200-49365600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:49336400-49351600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:49338200-49361600	Weak transcription	Stomach Mucosa	stomach
45	chr3:49338200-49375000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:49338600-49351600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:49343400-49351600	Weak transcription	HMEC	breast
48	chr3:49343600-49351600	Weak transcription	K562	blood
49	chr3:49344200-49351600	Weak transcription	NHDF-Ad	bronchial
50	chr3:49345000-49349800	Strong transcription	Brain Angular Gyrus	brain

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