Variant report

Variant	rs878546
Chromosome Location	chr11:17554930-17554931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10766409	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832797	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024319	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041027	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237956	0.89[ASN][1000 genomes]
rs2237957	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237959	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6486378	0.87[ASN][1000 genomes]
rs6486379	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs732983	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878547	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs878546	USH1C	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
2	chr11:17541600-17555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:17547200-17563200	Genic enhancers	Fetal Intestine Small	intestine
4	chr11:17551600-17556200	Genic enhancers	Fetal Intestine Large	intestine
5	chr11:17552800-17555400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:17553000-17555200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:17553400-17555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:17553600-17555000	Bivalent Enhancer	HepG2	liver
9	chr11:17553600-17557000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:17553600-17557200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:17553600-17561800	Weak transcription	Gastric	stomach
12	chr11:17553600-17562200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:17553800-17555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:17553800-17556600	Weak transcription	Brain Anterior Caudate	brain
15	chr11:17553800-17556800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:17553800-17558200	Weak transcription	Stomach Mucosa	stomach
17	chr11:17553800-17558600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:17553800-17563200	Weak transcription	Colonic Mucosa	Colon
19	chr11:17554000-17555000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr11:17554600-17556000	Flanking Active TSS	Hela-S3	cervix
21	chr11:17554800-17555000	Enhancers	Fetal Brain Male	brain
22	chr11:17554800-17555600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr11:17554800-17555800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr11:17554800-17556000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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