Variant report

Variant	rs512431
Chromosome Location	chr15:43541939-43541940
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43531183..43533744-chr15:43541275..43544195,2	K562	blood:
2	chr15:43524049..43526338-chr15:43541449..43544055,2	K562	blood:
3	chr15:43535426..43538797-chr15:43540482..43544036,3	K562	blood:
4	chr15:43536398..43537938-chr15:43540346..43541943,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104055	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1095389	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853991	0.93[EUR][1000 genomes]
rs12102205	0.81[AMR][1000 genomes]
rs12148735	0.84[AMR][1000 genomes]
rs1814323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278856	0.82[AMR][1000 genomes]
rs2412781	0.81[AMR][1000 genomes]
rs35278581	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809482	0.81[AMR][1000 genomes]
rs4547312	0.81[AMR][1000 genomes]
rs471122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs473016	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs473554	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475227	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs475261	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478028	0.82[AMR][1000 genomes]
rs485148	0.82[AMR][1000 genomes]
rs491800	0.81[AMR][1000 genomes]
rs491804	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs492743	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493444	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs498227	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs505249	1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs507178	0.83[AMR][1000 genomes]
rs510108	0.84[AMR][1000 genomes]
rs512628	0.83[AMR][1000 genomes]
rs513970	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs518234	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs518261	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs523737	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs526292	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs530188	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530683	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs531910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs538238	0.86[JPT][hapmap]
rs546722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs552701	0.81[AMR][1000 genomes]
rs554001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs555001	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs556851	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs560134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs564946	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs565658	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs567357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs572959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs573169	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs573615	0.82[AMR][1000 genomes]
rs574065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs576557	0.84[AMR][1000 genomes]
rs579651	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs825733	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs825734	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs512431	ADAL	cis	Adipose Subcutaneous	GTEx
rs512431	TGM5	cis	multi-tissue	Pritchard
rs512431	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs512431	ENSG00000104055	cis	multi-tissue	Pritchard
rs512431	ADAL	cis	Nerve Tibial	GTEx
rs512431	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs512431	TGM7	cis	Esophagus Mucosa	GTEx
rs512431	AC011330.5	cis	Artery Tibial	GTEx
rs512431	ZSCAN29	cis	Thyroid	GTEx
rs512431	ADAL	cis	lung	GTEx
rs512431	ADAL	cis	Artery Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43536800-43543400	Weak transcription	Esophagus	oesophagus
2	chr15:43538000-43546600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr15:43540400-43542600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:43540800-43542800	Enhancers	Primary hematopoietic stem cells	blood
5	chr15:43541000-43542600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:43541000-43542600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:43541000-43542800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:43541200-43542000	Enhancers	Osteobl	bone
9	chr15:43541200-43542400	Enhancers	NH-A	brain
10	chr15:43541200-43542600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:43541200-43542800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:43541200-43543200	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr15:43541400-43542400	Flanking Active TSS	GM12878-XiMat	blood
14	chr15:43541600-43542400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:43541600-43542400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr15:43541600-43542600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr15:43541600-43544400	Enhancers	K562	blood
18	chr15:43541800-43542000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:43541800-43542200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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