Variant report

Variant	rs60106007
Chromosome Location	chr12:48509764-48509765
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	STAT3	chr12:48509616-48509792	MCF10A-Er-Src	breast:	n/a	n/a
2	SPI1	chr12:48509619-48510024	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48498261..48500251-chr12:48508145..48510473,2	K562	blood:

Variant related genes	Relation type
PFKM	TF binding region
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10082861	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10219623	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10219645	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875745	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875746	0.95[ASN][1000 genomes]
rs10875747	0.97[ASN][1000 genomes]
rs10875748	0.97[ASN][1000 genomes]
rs10875750	0.95[ASN][1000 genomes]
rs10875756	0.87[ASN][1000 genomes]
rs11168413	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168414	0.97[ASN][1000 genomes]
rs11168415	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168418	0.97[ASN][1000 genomes]
rs11168420	0.90[ASN][1000 genomes]
rs11168421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168422	0.97[ASN][1000 genomes]
rs11168425	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168427	0.94[ASN][1000 genomes]
rs11168433	0.87[ASN][1000 genomes]
rs12297470	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12306290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12310813	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12312134	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17122666	0.91[ASN][1000 genomes]
rs1859445	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107638	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228500	0.97[ASN][1000 genomes]
rs2269933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269935	0.97[ASN][1000 genomes]
rs2286021	0.95[ASN][1000 genomes]
rs4760619	0.90[ASN][1000 genomes]
rs4760681	0.95[ASN][1000 genomes]
rs4760684	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760687	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760689	0.87[ASN][1000 genomes]
rs4760690	0.87[ASN][1000 genomes]
rs61343568	0.94[ASN][1000 genomes]
rs725454	0.91[ASN][1000 genomes]
rs7485355	0.95[ASN][1000 genomes]
rs7486424	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8804	0.95[ASN][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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs60106007	RP1-228P16.1	cis	Artery Tibial	GTEx
rs60106007	RP1-228P16.1	cis	Thyroid	GTEx
rs60106007	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48501200-48512200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr12:48505200-48512000	Weak transcription	Hela-S3	cervix
3	chr12:48509200-48511600	Weak transcription	K562	blood

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