Variant report

Variant	rs10766409
Chromosome Location	chr11:17555865-17555866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr11:17555277-17555908	Hela-S3	cervix:	n/a	n/a
2	SMARCC1	chr11:17555236-17555968	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:17555864-17555914	SKMC	muscle:	n/a
2	chr11:17555864-17555914	HEK293	kidney:	embryo
3	chr11:17555864-17555914	HCF	heart:	n/a
4	chr11:17555864-17555914	SK-N-MC	brain:	n/a
5	chr11:17555864-17555914	HRE	kidney:	n/a
6	chr11:17555864-17555914	RPTEC	kidney:	n/a
7	chr11:17555864-17555914	HPAEpiC	pulmonary alveolar:	n/a
8	chr11:17555864-17555914	GM12892	blood:	n/a
9	chr11:17555864-17555914	AG09319	gingival:	n/a
10	chr11:17555864-17555914	H1-hESC	embryonic stem cell:	embryo
11	chr11:17555864-17555914	NHDF-neo	bronchial:	n/a
12	chr11:17555864-17555914	HCM	heart:	n/a
13	chr11:17555864-17555914	HCT-116	colon:	n/a
14	chr11:17555864-17555914	MCF10A-Er-Src	breast:	n/a
15	chr11:17555864-17555914	Hela-S3	cervix:	n/a
16	chr11:17555864-17555914	HCPEpiC	choroid plexus:	n/a
17	chr11:17555864-17555914	NT2-D1	testis:	n/a
18	chr11:17555864-17555914	BJ	skin:	n/a
19	chr11:17555864-17555914	GM19239	blood:	n/a
20	chr11:17555864-17555914	LNCaP	prostate:	n/a
21	chr11:17555864-17555914	NB4	blood:	n/a
22	chr11:17555864-17555914	AG04449	skin:	fetal
23	chr11:17555864-17555914	HRPEpiC	eye:	n/a
24	chr11:17555864-17555914	HIPEpiC	eye:	n/a
25	chr11:17555864-17555914	HL-60	blood:	n/a
26	chr11:17555864-17555914	HRCEpiC	kidney:	n/a
27	chr11:17555864-17555914	AG04450	lung:	fetal
28	chr11:17555864-17555914	PANC-1	pancreas:	n/a
29	chr11:17555864-17555914	CMK	blood:	n/a
30	chr11:17555864-17555914	SK-N-SH	brain:	n/a
31	chr11:17555864-17555914	Caco-2	colon:	n/a
32	chr11:17555864-17555914	AG10803	skin:	n/a
33	chr11:17555864-17555914	T-47D	breast:	n/a
34	chr11:17555864-17555914	SK-N-SH_RA	brain:	n/a
35	chr11:17555864-17555914	GM06990	blood:	n/a
36	chr11:17555864-17555914	PrEC	prostate:	n/a
37	chr11:17555864-17555914	PFSK-1	brain:	n/a
38	chr11:17555864-17555914	HAEpiC	amniotic membrane:	n/a
39	chr11:17555864-17555914	ProgFib	skin:	n/a
40	chr11:17555864-17555914	Jurkat	blood:	n/a
41	chr11:17555864-17555914	U87	brain:	n/a
42	chr11:17555864-17555914	AoSMC	blood vessel:	n/a
43	chr11:17555864-17555914	BE2_C	brain:	n/a
44	chr11:17555864-17555914	GM12891	blood:	n/a
45	chr11:17555864-17555914	NHBE	bronchial:	n/a
46	chr11:17555864-17555914	K562	blood:	n/a
47	chr11:17555864-17555914	HUVEC	blood vessel:	n/a
48	chr11:17555864-17555914	Hepatocyte	liver:	n/a
49	chr11:17555864-17555914	ECC-1	luminal epithelium:	n/a
50	chr11:17555864-17555914	IMR90	lung:	fetal

No data

Variant related genes	Relation type
USH1C	TF binding region
USH1C	CpG island

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10741729	0.80[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs10832797	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024319	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041027	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237956	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2237957	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]
rs2237959	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]
rs4757539	0.84[CEU][hapmap]
rs6486378	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6486379	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7111978	0.83[AFR][1000 genomes]
rs7125811	0.91[AFR][1000 genomes]
rs732983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878546	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878547	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]

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
rs10766409	USH1C	cis	Thyroid	GTEx

Chromatin state (count:18 , 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	chr11:17551600-17556200	Genic enhancers	Fetal Intestine Large	intestine
4	chr11:17553600-17557000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:17553600-17557200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:17553600-17561800	Weak transcription	Gastric	stomach
7	chr11:17553600-17562200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:17553800-17556600	Weak transcription	Brain Anterior Caudate	brain
9	chr11:17553800-17556800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:17553800-17558200	Weak transcription	Stomach Mucosa	stomach
11	chr11:17553800-17558600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:17553800-17563200	Weak transcription	Colonic Mucosa	Colon
13	chr11:17554600-17556000	Flanking Active TSS	Hela-S3	cervix
14	chr11:17554800-17556000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:17555000-17556200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr11:17555400-17560400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:17555800-17556000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:17555800-17562400	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links