Variant report

Variant	rs2237957
Chromosome Location	chr11:17559018-17559019
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17554291..17557125-chr11:17558715..17560348,2	MCF-7	breast:
2	chr11:17557311..17560136-chr11:17561870..17563782,2	K562	blood:
3	chr11:17558247..17559969-chr11:17568227..17570175,2	K562	blood:

Variant related genes	Relation type
ENSG00000006611	Chromatin interaction
ENSG00000188162	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10741729	0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10766409	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832797	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024319	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041027	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237956	0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2237958	0.80[ASN][1000 genomes]
rs2237959	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]
rs2240489	0.87[CHB][hapmap]
rs2883581	0.83[CHB][hapmap]
rs4757540	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs6486378	0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6486379	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7102246	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs7106302	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs7111978	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7113935	0.87[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs7125811	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs732983	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs878546	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs878547	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]
rs972676	0.82[CHB][hapmap];0.82[CHD][hapmap]

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
rs2237957	USH1C	cis	Thyroid	GTEx

Chromatin state (count:12 , 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	chr11:17553600-17561800	Weak transcription	Gastric	stomach
4	chr11:17553600-17562200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:17553800-17563200	Weak transcription	Colonic Mucosa	Colon
6	chr11:17555400-17560400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr11:17555800-17562400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:17558000-17563400	Weak transcription	Hela-S3	cervix
9	chr11:17558200-17559800	Enhancers	Stomach Mucosa	stomach
10	chr11:17558400-17563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:17558800-17562200	Genic enhancers	Fetal Intestine Large	intestine
12	chr11:17559000-17561800	Weak transcription	Rectal Mucosa Donor 31	rectum

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