Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:43559220-43559370	HEEpiC	esophagus:	n/a	n/a
2	CTCF	chr15:43559180-43559330	HFF-Myc	foreskin:	n/a	n/a
3	TCF7L2	chr15:43559115-43559435	Hela-S3	cervix:	n/a	n/a
4	FOS	chr15:43559086-43559422	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr15:43559089-43559565	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr15:43559028-43559428	MCF10A-Er-Src	breast:	n/a	chr15:43559329-43559337
7	CEBPB	chr15:43559172-43559513	HepG2	liver:	n/a	n/a
8	FOS	chr15:43559107-43559344	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr15:43559141-43559503	Hela-S3	cervix:	n/a	n/a
10	SMC3	chr15:43559121-43559276	Hela-S3	cervix:	n/a	n/a
11	USF2	chr15:43559113-43559311	Hela-S3	cervix:	n/a	n/a
12	MYC	chr15:43559102-43559434	MCF10A-Er-Src	breast:	n/a	n/a
13	E2F4	chr15:43559182-43559509	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr15:43559103-43559400	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr15:43559190-43559498	K562	blood:	n/a	n/a
16	STAT3	chr15:43559094-43559395	MCF10A-Er-Src	breast:	n/a	chr15:43559329-43559337
17	STAT3	chr15:43559026-43559415	MCF10A-Er-Src	breast:	n/a	chr15:43559329-43559337
18	CEBPB	chr15:43559134-43559535	MCF-7	breast:	n/a	n/a
19	STAT3	chr15:43559026-43559407	MCF10A-Er-Src	breast:	n/a	chr15:43559329-43559337
20	FOS	chr15:43559122-43559466	MCF10A-Er-Src	breast:	n/a	n/a
21	MAX	chr15:43559150-43559353	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr15:43559224-43559433	IMR90	lung:	n/a	n/a
23	ZNF143	chr15:43559157-43559306	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43476285..43479868-chr15:43558571..43560739,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNDBP1-4	chr15:43557259-43559234	ucscGeneNc_uc001zvi_1

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12909095	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12911132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17779494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445909	1.00[ASN][1000 genomes]
rs66651343	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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

Variant related diseases (count:1)

Disease	PMID	Source
Lung cancer	19654303	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs748404	MGA	cis	parietal	SCAN
rs748404	ZSCAN29	cis	lymphoblastoid	seeQTL
rs748404	WDR76	cis	parietal	SCAN
rs748404	ZSCAN29	cis	multi-tissue	Pritchard
rs748404	TGM5	cis	lymphoblastoid	seeQTL
rs748404	TGM7	cis	Esophagus Mucosa	GTEx
rs748404	TGM5	cis	multi-tissue	Pritchard
rs748404	RTF1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43551600-43565600	Weak transcription	Right Atrium	heart
2	chr15:43556400-43560800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:43558600-43559400	Enhancers	Gastric	stomach
4	chr15:43558600-43560000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:43558600-43560000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr15:43558800-43559600	Bivalent Enhancer	NHEK	skin
7	chr15:43558800-43559800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:43558800-43560000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:43559000-43559400	Active TSS	Esophagus	oesophagus
10	chr15:43559000-43559600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:43559000-43559800	Enhancers	Stomach Mucosa	stomach
12	chr15:43559000-43562400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr15:43559200-43559400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:43559200-43559600	Flanking Active TSS	Hela-S3	cervix
15	chr15:43559200-43559600	Enhancers	HMEC	breast

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