Variant report

Variant	rs10117451
Chromosome Location	chr9:116035890-116035891
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:116035800-116035950	MCF-7	breast:	n/a	n/a
2	CHD1	chr9:116035600-116039131	IMR90	lung:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116035093..116036761-chr9:116347708..116350133,2	K562	blood:
2	chr9:116035655..116037372-chr9:116289546..116291507,2	K562	blood:
3	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
4	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
5	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
6	chr9:116035030..116037849-chr9:116344314..116346129,2	K562	blood:
7	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
8	chr9:115983488..115985496-chr9:116035418..116038927,3	MCF-7	breast:
9	chr9:116035314..116038256-chr9:116326581..116329349,2	K562	blood:

No data

Variant related genes	Relation type
PRPF4	TF binding region
ENSG00000136868	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000119321	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10759638	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10817474	0.80[ASN][1000 genomes]
rs10981710	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10981715	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11552582	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11789755	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12343629	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296073	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3750532	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3750533	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3750534	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4979231	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4979233	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6478000	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7027833	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7849326	0.87[EUR][1000 genomes];0.87[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10117451	CDC26	cis	Esophagus Muscularis	GTEx
rs10117451	PRPF4	cis	Thyroid	GTEx
rs10117451	BSPRY	cis	Heart Left Ventricle	GTEx
rs10117451	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs10117451	CDC26	cis	Heart Left Ventricle	GTEx
rs10117451	CDC26	cis	Thyroid	GTEx
rs10117451	CDC26	cis	Esophagus Mucosa	GTEx
rs10117451	CDC26	cis	Artery Tibial	GTEx
rs10117451	CDC26	cis	Adipose Subcutaneous	GTEx
rs10117451	CDC26	cis	lung	GTEx
rs10117451	CDC26	cis	Muscle Skeletal	GTEx
rs10117451	CDC26	cis	Nerve Tibial	GTEx
rs10117451	CDC26	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:116018600-116036000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:116021000-116036000	Strong transcription	Fetal Stomach	stomach
4	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
5	chr9:116022800-116036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:116026800-116036000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:116027200-116036000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr9:116027200-116036000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr9:116027200-116036200	Strong transcription	Primary T cells from cord blood	blood
11	chr9:116027400-116036000	Strong transcription	Fetal Muscle Leg	muscle
12	chr9:116027800-116036200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:116028000-116036000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr9:116028400-116036000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr9:116028400-116036000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:116028400-116036200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:116028600-116036000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:116028600-116036000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr9:116028600-116036000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr9:116028600-116036000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:116028600-116036000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:116028600-116036000	Strong transcription	Placenta	Placenta
23	chr9:116029000-116036000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:116029000-116036000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:116029600-116036000	Strong transcription	Fetal Lung	lung
26	chr9:116029600-116036000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr9:116029800-116036000	Strong transcription	Brain Anterior Caudate	brain
28	chr9:116029800-116036000	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:116029800-116036000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr9:116029800-116036000	Strong transcription	Osteobl	bone
31	chr9:116030000-116036000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:116030400-116036000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:116031000-116036000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:116031600-116036000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:116031600-116036000	Strong transcription	Hela-S3	cervix
36	chr9:116031600-116036000	Strong transcription	K562	blood
37	chr9:116031600-116036200	Strong transcription	Brain Hippocampus Middle	brain
38	chr9:116031800-116036000	Strong transcription	NHLF	lung
39	chr9:116032200-116036000	Strong transcription	NHEK	skin
40	chr9:116032400-116036000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr9:116032600-116036000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:116032600-116036000	Strong transcription	Fetal Intestine Large	intestine
43	chr9:116032600-116036000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr9:116033000-116036000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:116033000-116036000	Strong transcription	Liver	Liver
46	chr9:116033600-116036400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr9:116033800-116036800	Weak transcription	Psoas Muscle	Psoas
48	chr9:116034200-116036200	Weak transcription	HSMM	muscle
49	chr9:116034200-116036400	Weak transcription	Fetal Kidney	kidney
50	chr9:116034200-116036600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links