Variant report

Variant	rs473554
Chromosome Location	chr15:43568207-43568208
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	chr15:43565402..43569124-chr15:43569756..43572834,3	K562	blood:
2	chr15:43529509..43532294-chr15:43567272..43569682,2	K562	blood:

Variant related genes	Relation type
ENSG00000104055	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1095389	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853991	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1814323	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35278581	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs471122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs473016	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475227	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475261	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs491804	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492743	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs493177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493444	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498227	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs501884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs504417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs505249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512431	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs513970	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518234	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518261	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs523737	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs524547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs526292	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs530188	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs530683	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]
rs531910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538238	0.81[JPT][hapmap]
rs546722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs554001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555001	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556851	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs560134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564946	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565658	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs567357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs573169	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs574065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs579651	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs825733	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs825734	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs473554	TGM5	cis	Lymphoblastoid	GTEx
rs473554	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs473554	ADAL	cis	Nerve Tibial	GTEx
rs473554	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs473554	ADAL	cis	Adipose Subcutaneous	GTEx
rs473554	TGM5	cis	multi-tissue	Pritchard
rs473554	ADAL	cis	Artery Tibial	GTEx
rs473554	ADAL	cis	lung	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43565400-43568800	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr15:43565400-43570600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr15:43565400-43570800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr15:43565800-43569600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:43566000-43568600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:43566200-43574600	Weak transcription	Gastric	stomach
7	chr15:43566600-43569200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:43566600-43570200	Weak transcription	Esophagus	oesophagus
9	chr15:43567400-43568400	Enhancers	Brain Cingulate Gyrus	brain
10	chr15:43567800-43569000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:43568000-43568400	Enhancers	Psoas Muscle	Psoas
12	chr15:43568000-43568800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:43568000-43569000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:43568000-43569200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:43568200-43570200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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