Variant report

Variant	rs17831500
Chromosome Location	chr9:116047472-116047473
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116045466..116048065-chr9:116058989..116062588,3	MCF-7	breast:
2	chr9:116036500..116039891-chr9:116046406..116050157,5	MCF-7	breast:

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

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10123780	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10125030	0.91[EUR][1000 genomes]
rs10981723	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11789775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11791027	0.86[EUR][1000 genomes]
rs11794214	0.92[EUR][1000 genomes]
rs11794663	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12337498	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12337709	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12350705	0.89[EUR][1000 genomes]
rs17763934	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17764013	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087548	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810918	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3810919	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41307479	0.88[EUR][1000 genomes]
rs4979229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17831500	PRPF4	cis	lung	GTEx
rs17831500	PRPF4	cis	Thyroid	GTEx
rs17831500	CDC26	cis	Thyroid	GTEx
rs17831500	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs17831500	PRPF4	cis	Stomach	GTEx
rs17831500	CDC26	cis	Heart Left Ventricle	GTEx
rs17831500	CDC26	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116038600-116050400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:116038800-116048400	Weak transcription	Stomach Mucosa	stomach
3	chr9:116038800-116060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:116039000-116056800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:116039000-116058200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:116039200-116049400	Strong transcription	Fetal Intestine Small	intestine
7	chr9:116039400-116051000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr9:116039400-116055200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:116039400-116055800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:116039400-116056200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr9:116039400-116056400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:116039400-116056400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:116039400-116056400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:116039400-116056400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:116039400-116056600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:116039400-116056600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:116039400-116056600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr9:116039400-116056600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:116039400-116056600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:116039400-116056600	Strong transcription	Placenta	Placenta
21	chr9:116039400-116056600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:116039400-116056600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr9:116039400-116056800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:116039400-116056800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:116039600-116055600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:116039600-116055800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:116039600-116056000	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr9:116039600-116056000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:116039600-116056200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:116039600-116056400	Strong transcription	Fetal Lung	lung
31	chr9:116039600-116056600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:116039600-116056800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr9:116039600-116056800	Strong transcription	Fetal Stomach	stomach
34	chr9:116039800-116052000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:116039800-116054600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:116040000-116054800	Strong transcription	Lung	lung
37	chr9:116040000-116054800	Strong transcription	HSMMtube	muscle
38	chr9:116040000-116055800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr9:116040000-116056000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:116040000-116056400	Strong transcription	NH-A	brain
41	chr9:116040000-116056800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr9:116040200-116055400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr9:116040200-116056000	Strong transcription	HSMM	muscle
44	chr9:116040200-116056000	Strong transcription	NHEK	skin
45	chr9:116040200-116056200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:116040400-116051600	Strong transcription	K562	blood
47	chr9:116040400-116054800	Strong transcription	Colon Smooth Muscle	Colon
48	chr9:116040400-116055400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:116040400-116055600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr9:116040400-116055800	Strong transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links