Variant report

Variant	rs878547
Chromosome Location	chr11:17554510-17554511
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10741729	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs10766409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832797	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024319	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237956	0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2237957	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237959	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4757539	0.88[CEU][hapmap]
rs6486378	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6486379	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7111978	0.85[AFR][1000 genomes]
rs732983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878546	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
rs878547	USH1C	cis	Thyroid	GTEx

Chromatin state (count:25 , 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	chr11:17551400-17554800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:17551600-17556200	Genic enhancers	Fetal Intestine Large	intestine
6	chr11:17552000-17554600	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:17552400-17554600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:17552800-17555400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:17553000-17555200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:17553400-17554600	Weak transcription	Fetal Brain Male	brain
11	chr11:17553400-17555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr11:17553600-17555000	Bivalent Enhancer	HepG2	liver
13	chr11:17553600-17557000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:17553600-17557200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:17553600-17561800	Weak transcription	Gastric	stomach
16	chr11:17553600-17562200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:17553800-17554600	Enhancers	Hela-S3	cervix
18	chr11:17553800-17554800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr11:17553800-17555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:17553800-17556600	Weak transcription	Brain Anterior Caudate	brain
21	chr11:17553800-17556800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:17553800-17558200	Weak transcription	Stomach Mucosa	stomach
23	chr11:17553800-17558600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:17553800-17563200	Weak transcription	Colonic Mucosa	Colon
25	chr11:17554000-17555000	Weak transcription	Duodenum Mucosa	Duodenum

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