Variant report

Variant	rs10117906
Chromosome Location	chr9:116115438-116115439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116112976..116115054-chr9:116115085..116116590,2	K562	blood:
2	chr9:116110885..116114691-chr9:116115090..116117580,4	K562	blood:
3	chr9:116113999..116116348-chr9:116162534..116164296,2	MCF-7	breast:
4	chr9:116108846..116117047-chr9:116126327..116140994,30	MCF-7	breast:
5	chr9:116035712..116039392-chr9:116113201..116116002,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176386	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000148218	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10114327	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10118045	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118275	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10759640	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10759641	0.94[EUR][1000 genomes]
rs10817481	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10817485	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981763	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11787602	0.85[ASN][1000 genomes]
rs1998504	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2093691	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478002	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6478003	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6478004	0.84[ASN][1000 genomes]
rs6478005	0.84[ASN][1000 genomes]
rs6478006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025371	0.88[ASN][1000 genomes]
rs7025517	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7025770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7026076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041572	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7048039	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7849513	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7850002	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7850264	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7863921	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7864788	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7868271	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv519849	chr9:116111407-116144973	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10117906	PRPF4	cis	Esophagus Muscularis	GTEx
rs10117906	BSPRY	cis	Heart Left Ventricle	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116112800-116122800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:116113000-116135600	Weak transcription	Colonic Mucosa	Colon
3	chr9:116113000-116138000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:116113200-116117000	Weak transcription	Fetal Intestine Small	intestine
5	chr9:116113400-116116400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:116113400-116135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:116113800-116115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:116113800-116122200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:116113800-116137800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:116114000-116115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:116114000-116127400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr9:116114200-116136400	Weak transcription	Primary B cells from cord blood	blood
13	chr9:116114800-116115600	Enhancers	Pancreas	Pancrea
14	chr9:116115000-116121600	Weak transcription	Gastric	stomach
15	chr9:116115200-116119000	Weak transcription	HepG2	liver
16	chr9:116115200-116121000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:116115200-116121600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:116115400-116123400	Weak transcription	Stomach Mucosa	stomach
19	chr9:116115400-116135000	Weak transcription	Esophagus	oesophagus

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