Variant report

Variant	rs2883581
Chromosome Location	chr11:17555112-17555113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:17555029-17555170	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:17555063-17555113	HEEpiC	esophagus:	n/a
2	chr11:17555063-17555113	AoSMC	blood vessel:	n/a
3	chr11:17555063-17555113	HMEC	breast:	n/a
4	chr11:17555063-17555113	NT2-D1	testis:	n/a
5	chr11:17555063-17555113	NB4	blood:	n/a
6	chr11:17555063-17555113	HCF	heart:	n/a
7	chr11:17555063-17555113	SKMC	muscle:	n/a
8	chr11:17555063-17555113	AG10803	skin:	n/a
9	chr11:17555063-17555113	MCF10A-Er-Src	breast:	n/a
10	chr11:17555063-17555113	A549	lung:	n/a
11	chr11:17555063-17555113	SK-N-SH	brain:	n/a
12	chr11:17555063-17555113	Caco-2	colon:	n/a
13	chr11:17555063-17555113	CMK	blood:	n/a
14	chr11:17555063-17555113	HL-60	blood:	n/a
15	chr11:17555063-17555113	HNPCEpiC	eye:	n/a
16	chr11:17555063-17555113	U87	brain:	n/a
17	chr11:17555063-17555113	HCPEpiC	choroid plexus:	n/a
18	chr11:17555063-17555113	SAEC	small airway:	n/a
19	chr11:17555063-17555113	PANC-1	pancreas:	n/a
20	chr11:17555063-17555113	AG09309	skin:	n/a
21	chr11:17555063-17555113	HAEpiC	amniotic membrane:	n/a
22	chr11:17555063-17555113	BE2_C	brain:	n/a
23	chr11:17555063-17555113	GM12892	blood:	n/a
24	chr11:17555063-17555113	AG09319	gingival:	n/a
25	chr11:17555063-17555113	HepG2	liver:	n/a
26	chr11:17555063-17555113	GM06990	blood:	n/a
27	chr11:17555063-17555113	HEK293	kidney:	embryo
28	chr11:17555063-17555113	LNCaP	prostate:	n/a
29	chr11:17555063-17555113	BJ	skin:	n/a
30	chr11:17555063-17555113	NHBE	bronchial:	n/a
31	chr11:17555063-17555113	NH-A	brain:	n/a
32	chr11:17555063-17555113	H1-hESC	embryonic stem cell:	embryo
33	chr11:17555063-17555113	SK-N-SH_RA	brain:	n/a
34	chr11:17555063-17555113	HUVEC	blood vessel:	n/a
35	chr11:17555063-17555113	GM19239	blood:	n/a
36	chr11:17555063-17555113	GM12891	blood:	n/a
37	chr11:17555063-17555113	NHDF-neo	bronchial:	n/a
38	chr11:17555063-17555113	HRCEpiC	kidney:	n/a
39	chr11:17555063-17555113	HRE	kidney:	n/a
40	chr11:17555063-17555113	SK-N-MC	brain:	n/a
41	chr11:17555063-17555113	AG04449	skin:	fetal
42	chr11:17555063-17555113	AG04450	lung:	fetal
43	chr11:17555063-17555113	K562	blood:	n/a
44	chr11:17555063-17555113	PrEC	prostate:	n/a
45	chr11:17555063-17555113	PFSK-1	brain:	n/a
46	chr11:17555063-17555113	RPTEC	kidney:	n/a
47	chr11:17555063-17555113	Hepatocyte	liver:	n/a
48	chr11:17555063-17555113	HCT-116	colon:	n/a
49	chr11:17555063-17555113	Hela-S3	cervix:	n/a
50	chr11:17555063-17555113	ECC-1	luminal epithelium:	n/a

No data

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

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10741729	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs1859819	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073582	0.81[CEU][hapmap]
rs2108333	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2237955	0.96[ASN][1000 genomes]
rs2237957	0.83[CHB][hapmap]
rs2237958	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237959	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs2240489	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4756898	0.89[JPT][hapmap]
rs4757540	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7102246	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs7106302	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs7111978	0.86[ASN][1000 genomes]
rs7113935	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7116086	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7125811	0.87[ASN][1000 genomes]
rs7933452	0.96[ASN][1000 genomes]
rs972676	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[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
rs2883581	USH1C	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
2	chr11:17541600-17555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:17547200-17563200	Genic enhancers	Fetal Intestine Small	intestine
4	chr11:17551600-17556200	Genic enhancers	Fetal Intestine Large	intestine
5	chr11:17552800-17555400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:17553000-17555200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:17553400-17555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:17553600-17557000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:17553600-17557200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:17553600-17561800	Weak transcription	Gastric	stomach
11	chr11:17553600-17562200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:17553800-17555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:17553800-17556600	Weak transcription	Brain Anterior Caudate	brain
14	chr11:17553800-17556800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:17553800-17558200	Weak transcription	Stomach Mucosa	stomach
16	chr11:17553800-17558600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:17553800-17563200	Weak transcription	Colonic Mucosa	Colon
18	chr11:17554600-17556000	Flanking Active TSS	Hela-S3	cervix
19	chr11:17554800-17555600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr11:17554800-17555800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr11:17554800-17556000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:17555000-17555200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:17555000-17555400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr11:17555000-17556200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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