Variant report

Variant	rs2108333
Chromosome Location	chr11:17550138-17550139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:17405170..17406511-chr11:17549006..17550272,4	MCF-7	breast:
2	chr11:17375893..17376701-chr11:17549376..17550298,3	MCF-7	breast:
3	chr11:17404201..17406453-chr11:17548482..17550709,2	K562	blood:
4	chr11:17529263..17531115-chr11:17548910..17550754,2	K562	blood:
5	chr11:17376230..17376779-chr11:17549451..17550249,3	MCF-7	breast:
6	chr11:17550003..17552043-chr11:17563166..17565257,2	K562	blood:
7	chr11:17408129..17408789-chr11:17549376..17550314,3	K562	blood:
8	chr11:17538690..17542408-chr11:17546927..17550590,3	MCF-7	breast:
9	chr11:17405141..17406113-chr11:17549390..17550226,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000187486	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10741729	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs1859819	0.89[ASN][1000 genomes]
rs2237955	0.88[ASN][1000 genomes]
rs2237958	0.81[CEU][hapmap];0.90[ASN][1000 genomes]
rs2240489	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2883581	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4756898	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4757540	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7102246	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7106302	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7113935	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7933452	0.88[ASN][1000 genomes]
rs972676	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[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
rs2108333	USH1C	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
2	chr11:17531800-17552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
4	chr11:17540800-17552400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:17541000-17552600	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr11:17541400-17552400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:17541600-17551600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:17541600-17555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:17545400-17553000	Weak transcription	Gastric	stomach
10	chr11:17547200-17550400	Genic enhancers	Fetal Intestine Large	intestine
11	chr11:17547200-17563200	Genic enhancers	Fetal Intestine Small	intestine
12	chr11:17548000-17550200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr11:17549000-17550400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr11:17549000-17553400	Enhancers	Brain Cingulate Gyrus	brain
15	chr11:17549200-17550800	Enhancers	Brain Germinal Matrix	brain
16	chr11:17549200-17551400	Enhancers	HSMMtube	muscle
17	chr11:17549400-17550400	Enhancers	Duodenum Mucosa	Duodenum
18	chr11:17549400-17551000	Enhancers	Brain Hippocampus Middle	brain
19	chr11:17549400-17552600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr11:17549600-17551200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:17549600-17551600	Enhancers	Brain Anterior Caudate	brain
22	chr11:17549600-17551800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr11:17549600-17553000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr11:17549600-17553800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:17549800-17550200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr11:17549800-17550800	Weak transcription	Brain Angular Gyrus	brain
27	chr11:17549800-17551200	Enhancers	Fetal Heart	heart
28	chr11:17549800-17552600	Weak transcription	Colonic Mucosa	Colon
29	chr11:17549800-17553400	Enhancers	Fetal Brain Male	brain
30	chr11:17550000-17550400	Enhancers	Spleen	Spleen
31	chr11:17550000-17550600	Bivalent Enhancer	Adipose Nuclei	Adipose
32	chr11:17550000-17550800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:17550000-17550800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:17550000-17551000	Enhancers	Right Atrium	heart
35	chr11:17550000-17551000	Enhancers	HSMM	muscle
36	chr11:17550000-17551400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr11:17550000-17552000	Enhancers	Brain Substantia Nigra	brain
38	chr11:17550000-17552400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:17550000-17553800	Bivalent Enhancer	Fetal Muscle Leg	muscle

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