Variant report

Variant	rs17738890
Chromosome Location	chr9:16559835-16559836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10116857	0.82[EUR][1000 genomes]
rs10118895	0.88[EUR][1000 genomes]
rs10120281	0.82[EUR][1000 genomes]
rs10121959	0.81[EUR][1000 genomes]
rs10122372	0.88[EUR][1000 genomes]
rs10123515	0.90[EUR][1000 genomes]
rs10124530	0.86[EUR][1000 genomes]
rs10125014	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1029016	0.81[EUR][1000 genomes]
rs10738440	0.88[EUR][1000 genomes]
rs10756764	0.88[EUR][1000 genomes]
rs10756774	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10756775	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10962484	0.97[EUR][1000 genomes]
rs10962510	0.88[EUR][1000 genomes]
rs12004304	0.93[EUR][1000 genomes]
rs12339625	0.97[EUR][1000 genomes]
rs12340504	0.88[EUR][1000 genomes]
rs12350242	0.82[EUR][1000 genomes]
rs1415475	0.80[EUR][1000 genomes]
rs1538102	0.85[EUR][1000 genomes]
rs16934816	0.91[EUR][1000 genomes]
rs16934842	0.82[EUR][1000 genomes]
rs16934855	0.90[EUR][1000 genomes]
rs16934886	0.85[EUR][1000 genomes]
rs2095657	0.90[EUR][1000 genomes]
rs2149159	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28428651	0.97[EUR][1000 genomes]
rs28457730	0.89[EUR][1000 genomes]
rs28490464	0.82[EUR][1000 genomes]
rs28501274	0.93[EUR][1000 genomes]
rs28648047	0.97[EUR][1000 genomes]
rs28651010	0.95[EUR][1000 genomes]
rs4466493	0.80[EUR][1000 genomes]
rs4961725	0.84[EUR][1000 genomes]
rs56218971	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59379949	0.90[EUR][1000 genomes]
rs7018743	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7018877	0.84[EUR][1000 genomes]
rs7019016	0.84[EUR][1000 genomes]
rs7019105	0.84[EUR][1000 genomes]
rs7019625	0.88[EUR][1000 genomes]
rs7032239	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7032772	0.86[EUR][1000 genomes]
rs7036282	0.88[EUR][1000 genomes]
rs7048805	0.97[EUR][1000 genomes]
rs7049170	0.88[AMR][1000 genomes]
rs725011	0.82[EUR][1000 genomes]
rs73417477	0.97[EUR][1000 genomes]
rs7470623	0.82[EUR][1000 genomes]
rs7854979	0.84[EUR][1000 genomes]
rs7859395	0.95[EUR][1000 genomes]
rs7859971	0.89[EUR][1000 genomes]
rs7870508	0.86[EUR][1000 genomes]
rs7870730	0.85[EUR][1000 genomes]
rs7873338	0.90[EUR][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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16542600-16564000	Weak transcription	HUVEC	blood vessel
2	chr9:16543800-16567000	Weak transcription	HSMMtube	muscle
3	chr9:16546000-16568400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:16551800-16567800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:16552000-16567800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:16552800-16566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:16552800-16570200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:16552800-16571000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:16552800-16571400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:16553000-16570200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:16553000-16575200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:16554800-16561200	Weak transcription	Osteobl	bone
13	chr9:16556400-16560200	Weak transcription	Colonic Mucosa	Colon
14	chr9:16556400-16566000	Weak transcription	Fetal Stomach	stomach
15	chr9:16556400-16569200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:16556400-16570600	Weak transcription	NHLF	lung
17	chr9:16556400-16575600	Weak transcription	HSMM	muscle
18	chr9:16556600-16561000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:16559000-16560400	Enhancers	Colon Smooth Muscle	Colon
20	chr9:16559200-16560200	Enhancers	Ovary	ovary
21	chr9:16559400-16560600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr9:16559600-16560000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr9:16559600-16560000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr9:16559600-16560000	Enhancers	Small Intestine	intestine
25	chr9:16559600-16560200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:16559600-16560200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr9:16559600-16560200	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr9:16559600-16560400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr9:16559600-16561000	Enhancers	Liver	Liver
30	chr9:16559800-16560200	Enhancers	Psoas Muscle	Psoas
31	chr9:16559800-16560200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr9:16559800-16560200	Enhancers	Stomach Smooth Muscle	stomach
33	chr9:16559800-16560600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:16559800-16560800	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links