Variant report

Variant	rs10747788
Chromosome Location	chr12:58315338-58315339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58299223..58301569-chr12:58315233..58317786,2	K562	blood:
2	chr12:58313354..58316540-chr12:58327067..58330651,4	K562	blood:
3	chr12:58313751..58317468-chr12:58326546..58330746,3	K562	blood:
4	chr12:58313105..58315372-chr12:58334865..58337363,2	K562	blood:

Variant related genes	Relation type
ENSG00000166896	Chromatin interaction
ENSG00000257698	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10431506	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783857	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10783858	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877039	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877041	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172387	0.81[EUR][1000 genomes]
rs11172388	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172389	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2372309	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751325	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751326	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3751327	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4373979	0.81[EUR][1000 genomes]
rs4509811	0.81[EUR][1000 genomes]
rs4534624	0.81[EUR][1000 genomes]
rs4590915	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4630335	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4760174	0.81[EUR][1000 genomes]
rs4760344	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760346	0.80[EUR][1000 genomes]
rs6581159	0.83[CEU][hapmap]
rs7136981	0.81[EUR][1000 genomes]
rs7298370	0.81[EUR][1000 genomes]
rs7358584	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9971803	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10747788	XRCC6BP1	cis	normal skin	skin_eQTL
rs10747788	XRCC6BP1	cis	Nerve Tibial	GTEx
rs10747788	XRCC6BP1	cis	Artery Aorta	GTEx
rs10747788	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10747788	XRCC6BP1	cis	Whole Blood	GTEx
rs10747788	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs10747788	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10747788	XRCC6BP1	cis	lung	GTEx
rs10747788	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10747788	XRCC6BP1	cis	uninvolved skin	skin_eQTL
rs10747788	KUB3	cis	multi-tissue	Pritchard
rs10747788	XRCC6BP1	cis	lesional skin	skin_eQTL
rs10747788	XRCC6BP1	cis	Artery Tibial	GTEx
rs10747788	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10747788	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs10747788	XRCC6BP1	cis	Stomach	GTEx
rs10747788	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10747788	XRCC6BP1	cis	multi-tissue	Pritchard
rs10747788	XRCC6BP1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58312200-58325800	Weak transcription	Thymus	Thymus

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