Variant report

Variant	rs1859819
Chromosome Location	chr11:17566037-17566038
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:183)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr11:17565992-17566153	K562	blood:	n/a	n/a
2	JUND	chr11:17565913-17566113	K562	blood:	n/a	n/a
3	MAX	chr11:17565899-17566229	K562	blood:	n/a	n/a
4	POLR2A	chr11:17565691-17566221	HCT-116	colon:	n/a	n/a
5	MAFK	chr11:17566014-17566177	HepG2	liver:	n/a	chr11:17566039-17566053
6	HEY1	chr11:17565977-17566213	K562	blood:	n/a	n/a
7	POLR2A	chr11:17565653-17566219	HCT-116	colon:	n/a	n/a
8	E2F6	chr11:17565914-17566131	K562	blood:	n/a	chr11:17565989-17565999 chr11:17565964-17565973
9	MAFF	chr11:17566012-17566045	HepG2	liver:	n/a	n/a
10	MAZ	chr11:17565607-17566091	Hela-S3	cervix:	n/a	n/a
11	MAFK	chr11:17565922-17566131	Hela-S3	cervix:	n/a	chr11:17566039-17566053
12	POLR2A	chr11:17565981-17566167	K562	blood:	n/a	n/a
13	MAX	chr11:17565838-17566233	ECC-1	luminal epithelium:	n/a	n/a
14	SMC3	chr11:17566016-17566136	Hela-S3	cervix:	n/a	n/a
15	MAZ	chr11:17565870-17566266	K562	blood:	n/a	n/a
16	MAFK	chr11:17566028-17566122	HepG2	liver:	n/a	chr11:17566039-17566053
17	BACH1	chr11:17566012-17566149	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr11:17565949-17566199	K562	blood:	n/a	n/a
19	MAX	chr11:17565872-17566260	K562	blood:	n/a	n/a
20	RFX5	chr11:17565626-17566137	Hela-S3	cervix:	n/a	n/a
21	RCOR1	chr11:17566037-17566140	K562	blood:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:17566017-17566067	Caco-2	colon:	n/a
2	chr11:17566011-17566061	MCF-7	breast:	n/a
3	chr11:17566034-17566084	GM12878	blood:	n/a
4	chr11:17566034-17566084	PANC-1	pancreas:	n/a
5	chr11:17566034-17566084	HPAEpiC	pulmonary alveolar:	n/a
6	chr11:17566011-17566061	AG09319	gingival:	n/a
7	chr11:17566017-17566067	HepG2	liver:	n/a
8	chr11:17566034-17566084	SKMC	muscle:	n/a
9	chr11:17566017-17566067	CMK	blood:	n/a
10	chr11:17566034-17566084	SK-N-MC	brain:	n/a
11	chr11:17566011-17566061	HUVEC	blood vessel:	n/a
12	chr11:17566017-17566067	HMEC	breast:	n/a
13	chr11:17566034-17566084	HL-60	blood:	n/a
14	chr11:17566011-17566061	HL-60	blood:	n/a
15	chr11:17566034-17566084	U87	brain:	n/a
16	chr11:17566011-17566061	MCF10A-Er-Src	breast:	n/a
17	chr11:17566017-17566067	LNCaP	prostate:	n/a
18	chr11:17566011-17566061	HAEpiC	amniotic membrane:	n/a
19	chr11:17566011-17566061	SAEC	small airway:	n/a
20	chr11:17566034-17566084	HepG2	liver:	n/a
21	chr11:17566034-17566084	HIPEpiC	eye:	n/a
22	chr11:17566017-17566067	HEK293	kidney:	embryo
23	chr11:17566011-17566061	U87	brain:	n/a
24	chr11:17566017-17566067	ECC-1	luminal epithelium:	n/a
25	chr11:17566017-17566067	HRPEpiC	eye:	n/a
26	chr11:17566034-17566084	Hela-S3	cervix:	n/a
27	chr11:17566011-17566061	GM19239	blood:	n/a
28	chr11:17566011-17566061	AG09309	skin:	n/a
29	chr11:17566034-17566084	IMR90	lung:	fetal
30	chr11:17566011-17566061	GM06990	blood:	n/a
31	chr11:17566017-17566067	U87	brain:	n/a
32	chr11:17566011-17566061	HRPEpiC	eye:	n/a
33	chr11:17566017-17566067	HCT-116	colon:	n/a
34	chr11:17566034-17566084	BJ	skin:	n/a
35	chr11:17566011-17566061	HCM	heart:	n/a
36	chr11:17566017-17566067	K562	blood:	n/a
37	chr11:17566017-17566067	BE2_C	brain:	n/a
38	chr11:17566017-17566067	HCF	heart:	n/a
39	chr11:17566011-17566061	HCPEpiC	choroid plexus:	n/a
40	chr11:17566017-17566067	GM12892	blood:	n/a
41	chr11:17566011-17566061	HPAEpiC	pulmonary alveolar:	n/a
42	chr11:17566034-17566084	HRE	kidney:	n/a
43	chr11:17566017-17566067	HL-60	blood:	n/a
44	chr11:17566011-17566061	IMR90	lung:	fetal
45	chr11:17566017-17566067	SKMC	muscle:	n/a
46	chr11:17566011-17566061	HEK293	kidney:	embryo
47	chr11:17566034-17566084	Jurkat	blood:	n/a
48	chr11:17566011-17566061	HIPEpiC	eye:	n/a
49	chr11:17566034-17566084	AG10803	skin:	n/a
50	chr11:17566034-17566084	H1-hESC	embryonic stem cell:	embryo

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17563988..17566643-chr11:17568666..17571231,2	MCF-7	breast:

No data

Variant related genes	Relation type
USH1C	TF binding region
OTOG	TF binding region
OTOG	CpG island
USH1C	CpG island
ENSG00000188162	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10741729	0.88[ASN][1000 genomes]
rs2108333	0.89[ASN][1000 genomes]
rs2237955	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2237958	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237959	0.81[ASN][1000 genomes]
rs2883581	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4757540	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7102246	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7106302	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7111978	0.86[ASN][1000 genomes]
rs7113935	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7116086	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7125811	0.87[ASN][1000 genomes]
rs7933452	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs972676	0.95[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
rs1859819	USH1C	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17562400-17566200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr11:17563200-17566200	Active TSS	Rectal Smooth Muscle	rectum
3	chr11:17563600-17566400	Active TSS	Duodenum Mucosa	Duodenum
4	chr11:17563800-17566400	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr11:17564000-17566200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr11:17564800-17566200	Bivalent/Poised TSS	Small Intestine	intestine
7	chr11:17565000-17566200	Active TSS	A549	lung
8	chr11:17565000-17566400	Active TSS	Fetal Intestine Small	intestine
9	chr11:17565200-17566200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr11:17565200-17566200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr11:17565200-17566200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr11:17565400-17566200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr11:17565400-17566200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr11:17565400-17566200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr11:17565400-17566200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:17565400-17566200	Active TSS	Brain Anterior Caudate	brain
17	chr11:17565400-17566200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
18	chr11:17565400-17566200	Enhancers	Ovary	ovary
19	chr11:17565400-17566400	Bivalent Enhancer	Placenta	Placenta
20	chr11:17565600-17566200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr11:17565600-17566200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr11:17565600-17566200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:17565600-17566200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr11:17565600-17566200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:17565600-17566200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
26	chr11:17565600-17566200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:17565600-17566200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
28	chr11:17565600-17566200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:17565600-17566200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
30	chr11:17565600-17566200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
31	chr11:17565600-17566200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr11:17565600-17566200	Active TSS	Hela-S3	cervix
33	chr11:17565600-17566200	Active TSS	K562	blood
34	chr11:17565600-17566400	Active TSS	Fetal Intestine Large	intestine
35	chr11:17565800-17566200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr11:17565800-17566200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
37	chr11:17565800-17566200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:17565800-17566200	Enhancers	Lung	lung
39	chr11:17565800-17566400	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr11:17565800-17566400	Active TSS	Colonic Mucosa	Colon
41	chr11:17565800-17571000	Weak transcription	Right Atrium	heart
42	chr11:17566000-17566200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:17566000-17566200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:17566000-17566200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:17566000-17566200	Enhancers	Pancreas	Pancrea
46	chr11:17566000-17566200	Bivalent Enhancer	Right Ventricle	heart
47	chr11:17566000-17566200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
48	chr11:17566000-17568200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:17566000-17568400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:17566000-17568800	Weak transcription	Esophagus	oesophagus

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