Variant report

Variant	rs2041027
Chromosome Location	chr11:17553105-17553106
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	chr11:17099359..17101768-chr11:17550989..17553473,2	K562	blood:
2	chr11:17536439..17538354-chr11:17550411..17553263,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006611	Chromatin interaction

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

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

rs_ID	r²[population]
rs10741729	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap]
rs10766409	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]
rs10832797	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024319	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237956	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2237957	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237959	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4757539	0.88[CEU][hapmap]
rs6486378	0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6486379	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7111978	0.91[AFR][1000 genomes]
rs7125811	0.82[AFR][1000 genomes]
rs732983	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878546	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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
rs2041027	USH1C	cis	Thyroid	GTEx

Chromatin state (count:47 , 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	chr11:17549000-17553400	Enhancers	Brain Cingulate Gyrus	brain
5	chr11:17549600-17553800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:17549800-17553400	Enhancers	Fetal Brain Male	brain
7	chr11:17550000-17553800	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr11:17551400-17554800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:17551600-17556200	Genic enhancers	Fetal Intestine Large	intestine
10	chr11:17551800-17553400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:17552000-17553800	Enhancers	Brain Anterior Caudate	brain
12	chr11:17552000-17554600	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:17552200-17553800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr11:17552400-17553200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr11:17552400-17553200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr11:17552400-17553400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:17552400-17553600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr11:17552400-17553600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:17552400-17553600	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr11:17552400-17554600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:17552600-17553200	Active TSS	Spleen	Spleen
22	chr11:17552600-17553600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:17552600-17553600	Enhancers	Right Atrium	heart
24	chr11:17552600-17553800	Genic enhancers	Rectal Mucosa Donor 31	rectum
25	chr11:17552800-17553200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr11:17552800-17553400	Enhancers	Duodenum Mucosa	Duodenum
27	chr11:17552800-17553600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr11:17552800-17553600	Weak transcription	Brain Germinal Matrix	brain
29	chr11:17552800-17553600	Enhancers	Lung	lung
30	chr11:17552800-17553800	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr11:17552800-17553800	Flanking Active TSS	Hela-S3	cervix
32	chr11:17552800-17553800	Enhancers	HSMMtube	muscle
33	chr11:17552800-17553800	Enhancers	NH-A	brain
34	chr11:17552800-17555400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:17553000-17553200	Enhancers	Colonic Mucosa	Colon
36	chr11:17553000-17553200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr11:17553000-17553200	Enhancers	Fetal Thymus	thymus
38	chr11:17553000-17553400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr11:17553000-17553400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:17553000-17553600	Enhancers	Esophagus	oesophagus
41	chr11:17553000-17553600	Enhancers	Gastric	stomach
42	chr11:17553000-17553800	Enhancers	Brain Angular Gyrus	brain
43	chr11:17553000-17553800	Enhancers	Fetal Heart	heart
44	chr11:17553000-17553800	Enhancers	Left Ventricle	heart
45	chr11:17553000-17553800	Enhancers	Stomach Mucosa	stomach
46	chr11:17553000-17553800	Enhancers	HSMM	muscle
47	chr11:17553000-17555200	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links