Variant report

Variant	rs17134156
Chromosome Location	chr5:111481737-111481738
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:111474504..111476934-chr5:111480612..111482796,2	K562	blood:
2	chr5:111480523..111483778-chr5:111495014..111499185,3	K562	blood:
3	chr5:111480653..111483715-chr5:111488508..111491421,3	K562	blood:

Variant related genes	Relation type
ENSG00000224032	Chromatin interaction
ENSG00000238363	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10515438	1.00[CHB][hapmap]
rs17134152	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]
rs17134153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17134154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
rs17134157	0.87[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17266115	0.82[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs17651424	1.00[MEX][hapmap]
rs55641410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071312	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56092269	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57349429	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898536	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73227490	0.90[EUR][1000 genomes]
rs73227492	0.81[EUR][1000 genomes]
rs73227493	0.90[EUR][1000 genomes]
rs73227496	0.81[EUR][1000 genomes]
rs73227498	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73787775	0.81[EUR][1000 genomes]
rs73787779	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73787784	0.90[EUR][1000 genomes]
rs7730334	0.81[EUR][1000 genomes]
rs7731129	0.82[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
rs17134156	SNORA13	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111478800-111481800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr5:111479000-111481800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr5:111479200-111481800	Weak transcription	NHEK	skin
4	chr5:111479400-111482000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:111479600-111481800	Weak transcription	Fetal Stomach	stomach
6	chr5:111479600-111481800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:111479600-111482000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:111481200-111482800	Enhancers	Adipose Nuclei	Adipose
9	chr5:111481200-111482800	Enhancers	Fetal Lung	lung
10	chr5:111481200-111483200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:111481400-111482400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:111481400-111482800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:111481400-111482800	Enhancers	Fetal Heart	heart
14	chr5:111481400-111482800	Enhancers	NHLF	lung
15	chr5:111481400-111482800	Enhancers	Osteobl	bone
16	chr5:111481600-111481800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:111481600-111482000	Enhancers	NH-A	brain
18	chr5:111481600-111482600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:111481600-111482600	Enhancers	Fetal Muscle Leg	muscle
20	chr5:111481600-111482600	Enhancers	Rectal Smooth Muscle	rectum
21	chr5:111481600-111482600	Enhancers	HSMMtube	muscle
22	chr5:111481600-111482800	Flanking Active TSS	GM12878-XiMat	blood
23	chr5:111481600-111482800	Enhancers	HMEC	breast
24	chr5:111481600-111482800	Enhancers	NHDF-Ad	bronchial
25	chr5:111481600-111483000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links