Variant report

Variant	rs6475196
Chromosome Location	chr9:18061140-18061141
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1028962	0.80[AMR][1000 genomes]
rs1028963	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10738494	0.88[AMR][1000 genomes]
rs10810895	0.95[ASN][1000 genomes]
rs10810896	0.82[AMR][1000 genomes]
rs10963421	0.80[AMR][1000 genomes]
rs1360231	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1360232	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1411242	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1411244	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2077852	0.84[AMR][1000 genomes]
rs2186634	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2186635	0.85[AMR][1000 genomes]
rs7041361	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs725546	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7855468	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7866191	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7869628	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7872884	0.83[AMR][1000 genomes];0.82[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
rs6475196	ADAMTSL1	cis	cerebellum	SCAN
rs6475196	HAUS6	cis	cerebellum	SCAN
rs6475196	ACER2	cis	parietal	SCAN
rs6475196	TTC39B	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18038400-18061600	Weak transcription	Aorta	Aorta
2	chr9:18059200-18062000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:18059200-18063600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:18059400-18061200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:18059400-18061200	Weak transcription	Hela-S3	cervix
6	chr9:18059400-18061800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr9:18059800-18063600	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:18060000-18061800	Enhancers	Duodenum Mucosa	Duodenum
9	chr9:18060600-18061200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:18060600-18071400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:18060800-18061600	Enhancers	Fetal Heart	heart
12	chr9:18060800-18061600	Enhancers	Fetal Intestine Large	intestine
13	chr9:18061000-18061200	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr9:18061000-18061800	Enhancers	Fetal Intestine Small	intestine
15	chr9:18061000-18062000	Enhancers	Small Intestine	intestine

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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