Variant report

Variant	rs493444
Chromosome Location	chr15:43566470-43566471
allele	C/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:

Extended variants
information (count: 63 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1095389	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133395	0.81[AMR][1000 genomes]
rs11853991	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs12102205	0.83[AMR][1000 genomes]
rs12148735	0.86[AMR][1000 genomes]
rs1814323	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278856	0.84[AMR][1000 genomes]
rs2278857	0.82[AMR][1000 genomes]
rs2412781	0.83[AMR][1000 genomes]
rs35278581	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809482	0.83[AMR][1000 genomes]
rs4547312	0.83[AMR][1000 genomes]
rs471122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs473016	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs473554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475227	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475261	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs478028	0.84[AMR][1000 genomes]
rs485148	0.84[AMR][1000 genomes]
rs491800	0.83[AMR][1000 genomes]
rs491804	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492743	0.90[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];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs498227	0.92[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];1.00[AFR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507178	0.85[AMR][1000 genomes]
rs510108	0.86[AMR][1000 genomes]
rs512431	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs512628	0.85[AMR][1000 genomes]
rs513970	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.99[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	1.00[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[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs526292	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs530188	0.81[AFR][1000 genomes];1.00[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];0.91[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];0.90[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]
rs552701	0.83[AMR][1000 genomes]
rs554001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[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];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556851	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564946	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565658	0.90[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];1.00[AFR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs573169	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs573615	0.84[AMR][1000 genomes]
rs574065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs576557	0.86[AMR][1000 genomes]
rs579651	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493083	0.81[AMR][1000 genomes]
rs7166812	0.81[AMR][1000 genomes]
rs825733	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs825734	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920879	0.81[AMR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs493444	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs493444	ADAL	cis	Nerve Tibial	GTEx
rs493444	ZSCAN29	cis	Thyroid	GTEx
rs493444	ADAL	cis	Artery Tibial	GTEx
rs493444	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs493444	AC011330.5	cis	Artery Tibial	GTEx
rs493444	ADAL	cis	Adipose Subcutaneous	GTEx
rs493444	TGM7	cis	Esophagus Mucosa	GTEx
rs493444	TGM5	cis	multi-tissue	Pritchard
rs493444	ADAL	cis	lung	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43561400-43568000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:43563600-43566600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr15:43565200-43566600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr15:43565400-43568800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr15:43565400-43570600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:43565400-43570800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr15:43565600-43566600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:43565600-43566800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:43565600-43566800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr15:43565800-43568000	Weak transcription	Psoas Muscle	Psoas
11	chr15:43565800-43569600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr15:43566000-43568600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:43566200-43566600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:43566200-43566800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
15	chr15:43566200-43574600	Weak transcription	Gastric	stomach
16	chr15:43566400-43566600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:43566400-43566600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:43566400-43566600	Enhancers	Esophagus	oesophagus
19	chr15:43566400-43566600	Enhancers	Pancreas	Pancrea
20	chr15:43566400-43566800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:43566400-43566800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:43566400-43566800	Enhancers	HMEC	breast

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