Variant report

Variant	rs12592725
Chromosome Location	chr15:43516395-43516396
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	chr15:43516379-43516568	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43511739..43513912-chr15:43515291..43517866,3	K562	blood:
2	chr15:43513863..43516497-chr15:43519091..43522262,3	K562	blood:

Variant related genes	Relation type
EPB42	TF binding region
ENSG00000166947	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11070391	0.89[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs11070396	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070397	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11070398	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11855754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12899266	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1462856	0.89[CEU][hapmap];0.81[GIH][hapmap]
rs16957511	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1834643	0.92[EUR][1000 genomes]
rs2042742	0.94[EUR][1000 genomes]
rs2241516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28585036	0.83[ASW][hapmap];0.86[CEU][hapmap]
rs28756768	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2899077	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2947019	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34646108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736054	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap]
rs3784267	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784268	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924704	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap]
rs4924709	0.85[ASN][1000 genomes]
rs494863	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs495286	0.92[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs497138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs499280	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs530305	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs531850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs538218	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs540587	0.88[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes]
rs6493076	0.89[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap]
rs6493077	0.89[CEU][hapmap]
rs6493078	0.84[ASN][1000 genomes]
rs7174915	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7183814	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8027371	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9652444	0.92[ASW][hapmap]

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	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	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12592725	ELL3	cis	lymphoblastoid	seeQTL
rs12592725	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs12592725	C15orf63	cis	lymphoblastoid	seeQTL
rs12592725	CCNDBP1	cis	multi-tissue	Pritchard
rs12592725	TGM5	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43506400-43518600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:43511800-43526600	Weak transcription	Esophagus	oesophagus
3	chr15:43512600-43517800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:43513400-43517600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:43514000-43517600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:43514000-43522600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:43515000-43517600	Weak transcription	K562	blood

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