Variant report

Variant	rs2237959
Chromosome Location	chr11:17557017-17557018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:17556900-17557050	Caco-2	colon:	n/a	n/a

Variant related genes	Relation type
USH1C	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10741729	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10766409	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10832797	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024319	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1859819	0.81[ASN][1000 genomes]
rs2041027	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237955	0.82[ASN][1000 genomes]
rs2237956	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2237957	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237958	0.83[ASN][1000 genomes]
rs2240489	0.87[CHB][hapmap]
rs2883581	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs4757539	0.84[CEU][hapmap]
rs4757540	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs6486378	0.83[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6486379	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7102246	0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs7106302	0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs7111978	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7113935	0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs7116086	0.82[ASN][1000 genomes]
rs7125811	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs732983	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7933452	0.82[ASN][1000 genomes]
rs878546	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs878547	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]
rs972676	0.82[CHB][hapmap];0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2237959	SPON1	cis	parietal	SCAN
rs2237959	USH1C	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
2	chr11:17547200-17563200	Genic enhancers	Fetal Intestine Small	intestine
3	chr11:17553600-17557200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:17553600-17561800	Weak transcription	Gastric	stomach
5	chr11:17553600-17562200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr11:17553800-17558200	Weak transcription	Stomach Mucosa	stomach
7	chr11:17553800-17558600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:17553800-17563200	Weak transcription	Colonic Mucosa	Colon
9	chr11:17555400-17560400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:17555800-17562400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr11:17556000-17558000	Enhancers	Hela-S3	cervix
12	chr11:17556600-17557400	Enhancers	Brain Anterior Caudate	brain
13	chr11:17556800-17557400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr11:17556800-17557600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr11:17556800-17558800	Enhancers	Fetal Intestine Large	intestine

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