Variant report

Variant	rs17134152
Chromosome Location	chr5:111479955-111479956
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111478102..111480790-chr5:111495538..111497576,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224032	Chromatin interaction
ENSG00000238363	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10515438	1.00[CHB][hapmap]
rs17134153	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17134154	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17134155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17134156	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17266115	0.94[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17651424	0.83[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs27982	0.87[EUR][1000 genomes]
rs55641410	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071312	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56092269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57349429	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57541807	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60370278	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6898536	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73227490	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73227492	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73227493	0.82[EUR][1000 genomes]
rs73227496	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73227498	0.89[EUR][1000 genomes]
rs73787775	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73787779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73787782	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73787784	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7449256	0.88[AFR][1000 genomes]
rs7730334	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7731129	0.82[AMR][1000 genomes];0.88[EUR][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	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv599370	chr5:111419303-111485372	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17134152	SNORA13	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111477000-111480200	Enhancers	Fetal Heart	heart
2	chr5:111478400-111480200	Enhancers	Osteobl	bone
3	chr5:111478800-111481600	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:111478800-111481600	Weak transcription	NHDF-Ad	bronchial
5	chr5:111478800-111481800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:111479000-111481200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:111479000-111481200	Weak transcription	Adipose Nuclei	Adipose
8	chr5:111479000-111481400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:111479000-111481400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:111479000-111481600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:111479000-111481800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr5:111479200-111481800	Weak transcription	NHEK	skin
13	chr5:111479400-111482000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:111479600-111481200	Weak transcription	GM12878-XiMat	blood
15	chr5:111479600-111481600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:111479600-111481600	Weak transcription	HMEC	breast
17	chr5:111479600-111481800	Weak transcription	Fetal Stomach	stomach
18	chr5:111479600-111481800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:111479600-111482000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:111479800-111481200	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links