Variant report

Variant	rs7116086
Chromosome Location	chr11:17566450-17566451
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1859819	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237955	0.85[ASN][1000 genomes]
rs2237958	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237959	0.82[ASN][1000 genomes]
rs2883581	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4757540	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7102246	0.85[ASN][1000 genomes]
rs7106302	0.85[ASN][1000 genomes]
rs7113935	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7933452	0.85[ASN][1000 genomes]
rs972676	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1040065	chr11:17556031-17753467	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv7693	chr11:17556788-17601771	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1044126	chr11:17557715-17730646	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv540953	chr11:17557715-17730646	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv553586	chr11:17559018-17599093	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7116086	USH1C	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17565800-17571000	Weak transcription	Right Atrium	heart
2	chr11:17566000-17568200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:17566000-17568400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:17566000-17568800	Weak transcription	Esophagus	oesophagus
5	chr11:17566200-17567000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:17566200-17568200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:17566200-17568200	Weak transcription	Hela-S3	cervix
8	chr11:17566200-17568400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:17566200-17570400	Weak transcription	Pancreas	Pancrea
10	chr11:17566400-17566800	Enhancers	Fetal Intestine Large	intestine
11	chr11:17566400-17568600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:17566400-17568600	Weak transcription	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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