Variant report

Variant	rs491804
Chromosome Location	chr15:43560825-43560826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr15:43560780-43561408	ECC-1	luminal epithelium:	n/a	chr15:43561160-43561169 chr15:43561140-43561149 chr15:43561125-43561138
2	CTCF	chr15:43560822-43561501	SK-N-SH	brain:	n/a	chr15:43561128-43561141 chr15:43561121-43561142 chr15:43561126-43561144
3	RAD21	chr15:43560734-43561341	SK-N-SH	brain:	n/a	chr15:43561124-43561143
4	CTCF	chr15:43560780-43560930	GM12867	blood:	n/a	n/a
5	REST	chr15:43560764-43561427	HL-60	blood:	n/a	chr15:43561160-43561169 chr15:43561140-43561149 chr15:43561125-43561138
6	REST	chr15:43560796-43561420	ECC-1	luminal epithelium:	n/a	chr15:43561160-43561169 chr15:43561140-43561149 chr15:43561125-43561138
7	SMC3	chr15:43560805-43561460	SK-N-SH	brain:	n/a	chr15:43561128-43561142

No.	Distal block	Cell Line	Cell type
1	chr15:43500865..43501398-chr15:43560731..43561350,2	MCF-7	breast:
2	chr15:43517345..43518266-chr15:43560680..43561199,2	K562	blood:
3	chr15:43517417..43518218-chr15:43560788..43561555,3	MCF-7	breast:
4	chr15:43501002..43502077-chr15:43560347..43561187,3	MCF-7	breast:

Variant related genes	Relation type
TGM5	TF binding region
ATP5HP1	TF binding region
ENSG00000166947	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1095389	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11853991	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1814323	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35278581	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs471122	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473554	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475227	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493177	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493444	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs498227	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs501884	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504417	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505249	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512431	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs513970	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518234	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs518261	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs523737	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524547	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs526292	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530188	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs530683	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs546722	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554001	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555001	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556851	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs560134	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564946	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565658	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567357	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572959	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573169	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574065	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs579651	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs825733	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs825734	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs491804	TGM5	cis	multi-tissue	Pritchard
rs491804	ADAL	cis	Adipose Subcutaneous	GTEx
rs491804	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs491804	ADAL	cis	lung	GTEx
rs491804	ADAL	cis	Artery Tibial	GTEx
rs491804	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs491804	ADAL	cis	Nerve Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43551600-43565600	Weak transcription	Right Atrium	heart
2	chr15:43559000-43562400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr15:43559600-43561600	Enhancers	Esophagus	oesophagus
4	chr15:43560000-43565400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:43560400-43563600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr15:43560800-43561400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:43560800-43563800	Enhancers	Primary hematopoietic stem cells	blood

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