Variant report

Variant	rs4979233
Chromosome Location	chr9:116057781-116057782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116057494..116059760-chr9:116060068..116061932,2	K562	blood:
2	chr9:116057020..116059626-chr9:116062795..116064510,2	K562	blood:
3	chr9:116035504..116039547-chr9:116056957..116059661,4	K562	blood:
4	chr9:116056474..116058317-chr9:116067548..116069839,2	K562	blood:
5	chr9:116036613..116039490-chr9:116057156..116059661,3	K562	blood:
6	chr9:116054929..116058723-chr9:116059143..116063371,5	MCF-7	breast:
7	chr9:116036740..116039923-chr9:116057646..116061284,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165188	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000176386	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10117451	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10759638	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10817474	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs10817475	0.88[CEU][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10981710	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981712	0.81[EUR][1000 genomes]
rs10981715	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981720	0.81[EUR][1000 genomes]
rs11552582	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11789755	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12236683	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12343629	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296073	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3750532	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3750533	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750534	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750535	1.00[CEU][hapmap]
rs4979231	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979232	0.88[CEU][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6478000	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027833	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7847295	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7849326	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299214	1.00[CEU][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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4979233	CDC26	cis	lung	GTEx
rs4979233	CDC26	cis	Esophagus Muscularis	GTEx
rs4979233	CDC26	cis	Whole Blood	GTEx
rs4979233	CDC26	cis	Adipose Subcutaneous	GTEx
rs4979233	CDC26	cis	Artery Tibial	GTEx
rs4979233	PRPF4	cis	Thyroid	GTEx
rs4979233	CDC26	cis	Esophagus Mucosa	GTEx
rs4979233	BSPRY	cis	Heart Left Ventricle	GTEx
rs4979233	CDC26	cis	Muscle Skeletal	GTEx
rs4979233	CDC26	cis	Heart Left Ventricle	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116038800-116060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:116039000-116058200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:116050000-116062000	Weak transcription	Stomach Mucosa	stomach
4	chr9:116054200-116065000	Weak transcription	Fetal Kidney	kidney
5	chr9:116054600-116065200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:116054800-116057800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:116054800-116058000	Weak transcription	Lung	lung
8	chr9:116054800-116058400	Weak transcription	Ovary	ovary
9	chr9:116054800-116058600	Weak transcription	HSMMtube	muscle
10	chr9:116054800-116059600	Weak transcription	Small Intestine	intestine
11	chr9:116054800-116060600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:116054800-116062200	Weak transcription	Colonic Mucosa	Colon
13	chr9:116054800-116062200	Weak transcription	Pancreas	Pancrea
14	chr9:116054800-116065200	Weak transcription	Esophagus	oesophagus
15	chr9:116055000-116058000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:116055000-116058000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:116055000-116060200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:116055000-116063800	Weak transcription	Spleen	Spleen
19	chr9:116055200-116058200	Weak transcription	Brain Anterior Caudate	brain
20	chr9:116055200-116058200	Weak transcription	K562	blood
21	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:116055400-116058600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr9:116055600-116059400	Weak transcription	Hela-S3	cervix
24	chr9:116055600-116060000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:116055600-116062200	Weak transcription	A549	lung
26	chr9:116055800-116057800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:116055800-116057800	Weak transcription	Right Ventricle	heart
28	chr9:116055800-116058400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:116055800-116058600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:116055800-116059600	Weak transcription	Adipose Nuclei	Adipose
31	chr9:116055800-116061600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:116055800-116061800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr9:116055800-116062000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:116056000-116057800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:116056000-116057800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:116056000-116057800	Weak transcription	Left Ventricle	heart
37	chr9:116056000-116058000	Weak transcription	Fetal Intestine Small	intestine
38	chr9:116056000-116058000	Weak transcription	HepG2	liver
39	chr9:116056000-116058200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:116056000-116058200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:116056000-116058400	Weak transcription	NHEK	skin
42	chr9:116056000-116058600	Weak transcription	Osteobl	bone
43	chr9:116056000-116059000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:116056000-116059400	Weak transcription	NHLF	lung
45	chr9:116056000-116061000	Weak transcription	HSMM	muscle
46	chr9:116056000-116061200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:116056000-116062000	Weak transcription	Gastric	stomach
48	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
49	chr9:116056200-116057800	Weak transcription	Dnd41	blood
50	chr9:116056200-116058000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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