Variant report

Variant	rs10783860
Chromosome Location	chr12:58356391-58356392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58347570..58349774-chr12:58354574..58356685,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10747790	0.81[EUR][1000 genomes]
rs10783864	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877048	0.83[ASN][1000 genomes]
rs10877050	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10877053	0.80[EUR][1000 genomes]
rs10877055	0.81[EUR][1000 genomes]
rs10877056	0.81[EUR][1000 genomes]
rs11172389	0.80[AFR][1000 genomes]
rs11172408	0.87[ASN][1000 genomes]
rs11172419	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172425	0.81[EUR][1000 genomes]
rs11172427	0.81[EUR][1000 genomes]
rs11608333	0.87[ASN][1000 genomes]
rs11608939	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12366757	0.87[ASN][1000 genomes]
rs12366794	0.87[ASN][1000 genomes]
rs12368024	0.81[ASN][1000 genomes]
rs12580381	0.80[EUR][1000 genomes]
rs12820787	0.81[EUR][1000 genomes]
rs12825843	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12828647	0.81[ASN][1000 genomes]
rs1304496	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1354795	0.81[EUR][1000 genomes]
rs1466972	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1506890	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1605330	0.80[EUR][1000 genomes]
rs1605334	0.81[EUR][1000 genomes]
rs1605335	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17120134	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17120179	0.81[EUR][1000 genomes]
rs17120182	0.81[EUR][1000 genomes]
rs1848129	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1911258	0.81[EUR][1000 genomes]
rs1911259	0.81[EUR][1000 genomes]
rs1911260	0.81[EUR][1000 genomes]
rs1911261	0.81[EUR][1000 genomes]
rs2089377	0.82[EUR][1000 genomes]
rs2102349	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2372376	0.81[EUR][1000 genomes]
rs2372377	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2372378	0.87[ASN][1000 genomes]
rs2372379	0.87[ASN][1000 genomes]
rs2659639	0.83[AMR][1000 genomes]
rs2659659	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2659662	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659665	0.83[AMR][1000 genomes]
rs2717404	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2720181	0.83[AMR][1000 genomes]
rs2720191	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2888299	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34504532	0.81[EUR][1000 genomes]
rs35195629	0.81[EUR][1000 genomes]
rs35264128	0.81[EUR][1000 genomes]
rs3858557	0.85[ASN][1000 genomes]
rs3858558	0.85[ASN][1000 genomes]
rs3913866	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3933982	0.80[ASN][1000 genomes]
rs4403837	0.81[EUR][1000 genomes]
rs4435045	0.80[EUR][1000 genomes]
rs4604932	0.80[EUR][1000 genomes]
rs4760175	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7132521	0.87[ASN][1000 genomes]
rs7135328	0.81[EUR][1000 genomes]
rs7135728	0.81[EUR][1000 genomes]
rs7139165	0.81[EUR][1000 genomes]
rs7304628	0.81[EUR][1000 genomes]
rs7304755	0.80[EUR][1000 genomes]
rs7954291	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959747	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7960690	0.82[ASN][1000 genomes]
rs7960942	0.81[ASN][1000 genomes]
rs7970516	0.81[EUR][1000 genomes]
rs7972562	0.81[EUR][1000 genomes]
rs7977671	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978423	0.81[EUR][1000 genomes]
rs871907	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv523853	chr12:58350631-58386722	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv975500	chr12:58351052-58362673	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10783860	XRCC6BP1	cis	Artery Tibial	GTEx
rs10783860	XRCC6BP1	cis	Whole Blood	GTEx
rs10783860	XRCC6BP1	cis	Thyroid	GTEx
rs10783860	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10783860	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10783860	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10783860	XRCC6BP1	cis	lung	GTEx
rs10783860	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs10783860	XRCC6BP1	cis	Nerve Tibial	GTEx
rs10783860	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10783860	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10783860	XRCC6BP1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58336200-58359600	Weak transcription	A549	lung
2	chr12:58336400-58359600	Weak transcription	HMEC	breast
3	chr12:58337200-58358400	Weak transcription	HepG2	liver
4	chr12:58351200-58359400	Weak transcription	K562	blood
5	chr12:58352200-58358200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:58352400-58359400	Weak transcription	Placenta	Placenta
7	chr12:58352600-58357800	Weak transcription	Dnd41	blood

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