Variant report

Variant	rs10741729
Chromosome Location	chr11:17562113-17562114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17557311..17560136-chr11:17561870..17563782,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10766409	0.80[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs10766410	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs1859819	0.88[ASN][1000 genomes]
rs2041027	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap]
rs2108333	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs2237955	0.92[ASN][1000 genomes]
rs2237956	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237957	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]
rs2237958	0.90[ASN][1000 genomes]
rs2237959	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]
rs2240489	0.91[CHB][hapmap]
rs2883581	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs4757540	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs6486378	0.91[JPT][hapmap]
rs7102246	0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs7106302	0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs7111978	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7113935	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs7125811	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732983	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs7933452	0.92[ASN][1000 genomes]
rs878547	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs972676	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[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
rs10741729	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	chr11:17553600-17562200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr11:17553800-17563200	Weak transcription	Colonic Mucosa	Colon
5	chr11:17555800-17562400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:17558000-17563400	Weak transcription	Hela-S3	cervix
7	chr11:17558400-17563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:17558800-17562200	Genic enhancers	Fetal Intestine Large	intestine
9	chr11:17560200-17562200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr11:17560400-17562600	Enhancers	Duodenum Mucosa	Duodenum
11	chr11:17561800-17562200	Enhancers	Gastric	stomach
12	chr11:17561800-17562800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr11:17561800-17563000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr11:17562000-17564000	Enhancers	Stomach Mucosa	stomach
15	chr11:17562000-17565200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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