Variant report

Variant	rs560134
Chromosome Location	chr15:43555699-43555700
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43553124..43555754-chr15:43557859..43559411,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNDBP1-4	chr15:43555569-43555799	ucscGeneNc_uc001zvi_1

Variant related genes	Relation type
ENSG00000104055	Chromatin interaction

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];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133395	0.81[AMR][1000 genomes]
rs11853991	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs12102205	0.83[AMR][1000 genomes]
rs12148735	0.86[AMR][1000 genomes]
rs1814323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809482	0.83[AMR][1000 genomes]
rs4547312	0.83[AMR][1000 genomes]
rs471122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473016	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473554	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]
rs475227	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475261	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492743	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs498227	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs501884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507178	0.85[AMR][1000 genomes]
rs510108	0.86[AMR][1000 genomes]
rs512431	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]
rs512628	0.85[AMR][1000 genomes]
rs513970	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518234	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs518261	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs523737	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs526292	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530188	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs530683	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]
rs531910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs538238	0.86[JPT][hapmap]
rs546722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552701	0.83[AMR][1000 genomes]
rs554001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555001	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556851	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs564946	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565658	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573169	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs573615	0.84[AMR][1000 genomes]
rs574065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576557	0.86[AMR][1000 genomes]
rs579651	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493083	0.81[AMR][1000 genomes]
rs7166812	0.81[AMR][1000 genomes]
rs825733	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs825734	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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
rs560134	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs560134	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs560134	ZSCAN29	cis	Thyroid	GTEx
rs560134	ADAL	cis	lung	GTEx
rs560134	ADAL	cis	Artery Tibial	GTEx
rs560134	ADAL	cis	Adipose Subcutaneous	GTEx
rs560134	ADAL	cis	Nerve Tibial	GTEx
rs560134	AC011330.5	cis	Artery Tibial	GTEx
rs560134	TGM5	cis	multi-tissue	Pritchard
rs560134	TGM7	cis	Esophagus Mucosa	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43551600-43565600	Weak transcription	Right Atrium	heart
2	chr15:43554400-43557400	Weak transcription	Esophagus	oesophagus

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