Variant report

Variant	rs7125811
Chromosome Location	chr11:17565605-17565606
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	chr11:17563988..17566643-chr11:17568666..17571231,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188162	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10741729	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766409	0.91[AFR][1000 genomes]
rs10832797	0.85[AFR][1000 genomes]
rs12360902	0.84[EUR][1000 genomes]
rs1859819	0.87[ASN][1000 genomes]
rs2041027	0.82[AFR][1000 genomes]
rs2237955	0.91[ASN][1000 genomes]
rs2237956	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2237957	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2237958	0.89[ASN][1000 genomes]
rs2237959	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2883581	0.87[ASN][1000 genomes]
rs4757540	0.89[ASN][1000 genomes]
rs6486379	0.80[AFR][1000 genomes]
rs7102246	0.91[ASN][1000 genomes]
rs7106302	0.91[ASN][1000 genomes]
rs7111978	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7113935	0.89[ASN][1000 genomes]
rs7933452	0.91[ASN][1000 genomes]
rs972676	0.90[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
rs7125811	USH1C	cis	Thyroid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

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	chr11:17564000-17566000	Active TSS	Fetal Kidney	kidney
6	chr11:17564000-17566200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr11:17564200-17566000	Bivalent/Poised TSS	Fetal Stomach	stomach
8	chr11:17564400-17566000	Active TSS	Gastric	stomach
9	chr11:17564800-17565800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr11:17564800-17565800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
11	chr11:17564800-17566200	Bivalent/Poised TSS	Small Intestine	intestine
12	chr11:17565000-17566000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
13	chr11:17565000-17566200	Active TSS	A549	lung
14	chr11:17565000-17566400	Active TSS	Fetal Intestine Small	intestine
15	chr11:17565200-17565800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr11:17565200-17565800	Enhancers	Spleen	Spleen
17	chr11:17565200-17566000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:17565200-17566000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:17565200-17566000	Bivalent/Poised TSS	Stomach Mucosa	stomach
20	chr11:17565200-17566200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr11:17565200-17566200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr11:17565200-17566200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr11:17565400-17565800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
24	chr11:17565400-17565800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:17565400-17565800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr11:17565400-17565800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:17565400-17565800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:17565400-17565800	Bivalent/Poised TSS	Colonic Mucosa	Colon
29	chr11:17565400-17565800	Enhancers	Right Ventricle	heart
30	chr11:17565400-17566000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:17565400-17566000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:17565400-17566000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
33	chr11:17565400-17566200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
34	chr11:17565400-17566200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr11:17565400-17566200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr11:17565400-17566200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:17565400-17566200	Active TSS	Brain Anterior Caudate	brain
38	chr11:17565400-17566200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
39	chr11:17565400-17566200	Enhancers	Ovary	ovary
40	chr11:17565400-17566400	Bivalent Enhancer	Placenta	Placenta
41	chr11:17565600-17565800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr11:17565600-17565800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:17565600-17565800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:17565600-17565800	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr11:17565600-17565800	Enhancers	Right Atrium	heart
46	chr11:17565600-17566000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:17565600-17566000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:17565600-17566000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:17565600-17566000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:17565600-17566000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links