Variant report

Variant	rs11118879
Chromosome Location	chr1:222049433-222049434
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:221915847..221918268-chr1:222049176..222051061,2	K562	blood:
2	chr1:222045982..222047740-chr1:222048035..222050126,2	MCF-7	breast:
3	chr1:222047877..222050005-chr1:222054985..222056926,2	MCF-7	breast:
4	chr1:222047894..222050064-chr1:222050661..222052612,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10495181	0.87[AMR][1000 genomes]
rs10779461	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11118876	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11118878	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11118882	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583667	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11586814	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12027640	0.91[AMR][1000 genomes]
rs12562188	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12566801	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12567671	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12568711	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34224972	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6604679	0.90[ASN][1000 genomes]
rs6604680	0.90[ASN][1000 genomes]
rs6604682	0.98[ASN][1000 genomes]
rs7339876	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11118879	USH2A	cis	parietal	SCAN
rs11118879	C1orf115	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222040800-222049800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:222043200-222052800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:222043400-222051400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:222043400-222052600	Weak transcription	HSMMtube	muscle
5	chr1:222046600-222050200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:222047800-222050200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:222047800-222054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:222048000-222051400	Weak transcription	HMEC	breast
9	chr1:222048200-222050600	Weak transcription	GM12878-XiMat	blood
10	chr1:222048200-222051400	Weak transcription	Osteobl	bone
11	chr1:222048200-222052000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:222048200-222052400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:222048400-222049800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:222048400-222050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:222048400-222051400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:222048400-222051600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:222048600-222049800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:222048600-222051400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:222048600-222051400	Weak transcription	HSMM	muscle
20	chr1:222048600-222051400	Weak transcription	NH-A	brain
21	chr1:222048600-222051800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:222048600-222051800	Weak transcription	NHLF	lung
23	chr1:222048600-222073600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:222048800-222060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:222049000-222050000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:222049400-222050400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:222049400-222050400	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links