Variant report

Variant	rs725546
Chromosome Location	chr9:18057101-18057102
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1028962	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1028963	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738494	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10738496	0.87[EUR][1000 genomes]
rs10738497	0.87[EUR][1000 genomes]
rs10738498	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10810888	0.81[EUR][1000 genomes]
rs10810896	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10963402	0.82[EUR][1000 genomes]
rs1329921	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1360231	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1360232	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1411242	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1411244	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1411248	0.85[EUR][1000 genomes]
rs1419161	0.80[EUR][1000 genomes]
rs2077852	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2186634	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2186635	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4961455	0.84[EUR][1000 genomes]
rs6475196	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7021852	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7855468	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7865493	0.82[EUR][1000 genomes]
rs7866191	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7869628	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7872884	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9987604	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613706	chr9:17718918-18090934	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv613707	chr9:17720175-18070475	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv613708	chr9:17720175-18072085	Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1021605	chr9:18002205-18271109	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892678	chr9:18033944-18082567	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv466280	chr9:18033944-18166112	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv471288	chr9:18033944-18166112	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv613723	chr9:18033944-18166112	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv892679	chr9:18044802-18226609	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs725546	TTC39B	cis	cerebellum	SCAN
rs725546	HAUS6	cis	cerebellum	SCAN
rs725546	ADAMTSL1	cis	cerebellum	SCAN
rs725546	ACER2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18038400-18061600	Weak transcription	Aorta	Aorta
2	chr9:18056000-18058800	Weak transcription	Fetal Lung	lung
3	chr9:18056000-18059400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr9:18056400-18057200	Enhancers	Ovary	ovary
5	chr9:18056400-18057800	Enhancers	GM12878-XiMat	blood
6	chr9:18056600-18057200	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr9:18056600-18057400	Enhancers	Primary hematopoietic stem cells	blood
8	chr9:18057000-18057800	Weak transcription	Rectal Mucosa Donor 31	rectum

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