Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr16:55702160-55703165	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr16:55702059-55703447	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr16:55702227-55703253	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr16:55702752-55703076	HepG2	liver:	n/a	n/a
5	FOS	chr16:55702183-55703268	MCF10A-Er-Src	breast:	n/a	chr16:55702532-55702542 chr16:55702533-55702542 chr16:55702529-55702540 chr16:55702532-55702542 chr16:55702532-55702542 chr16:55702531-55702543 chr16:55702532-55702542
6	MYC	chr16:55702208-55703278	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr16:55702229-55703283	MCF10A-Er-Src	breast:	n/a	chr16:55702532-55702542 chr16:55702533-55702542 chr16:55702529-55702540 chr16:55702532-55702542 chr16:55702532-55702542 chr16:55702531-55702543 chr16:55702532-55702542
8	STAT3	chr16:55702234-55703254	MCF10A-Er-Src	breast:	n/a	n/a
9	E2F4	chr16:55702828-55703234	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr16:55702316-55703174	MCF10A-Er-Src	breast:	n/a	chr16:55702532-55702542 chr16:55702533-55702542 chr16:55702529-55702540 chr16:55702532-55702542 chr16:55702532-55702542 chr16:55702531-55702543 chr16:55702532-55702542
11	FOS	chr16:55702271-55703326	MCF10A-Er-Src	breast:	n/a	chr16:55702532-55702542 chr16:55702533-55702542 chr16:55702529-55702540 chr16:55702532-55702542 chr16:55702532-55702542 chr16:55702531-55702543 chr16:55702532-55702542
12	MYC	chr16:55702213-55703101	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr16:55703040-55703190	HMEC	breast:	n/a	n/a
14	STAT3	chr16:55702433-55703174	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:55460964..55463307-chr16:55702400..55704624,2	MCF-7	breast:
2	chr16:55695466..55697327-chr16:55702123..55704926,2	K562	blood:

Variant related genes	Relation type
SLC6A2	TF binding region

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11076111	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[EUR][1000 genomes]
rs12232407	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1362620	0.95[EUR][1000 genomes]
rs1362621	0.95[EUR][1000 genomes]
rs1532701	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs17247999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs17307096	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17307291	0.95[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs17841327	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2062723	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2242446	0.91[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs28386840	0.92[EUR][1000 genomes]
rs28501300	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28618083	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28665972	0.95[EUR][1000 genomes]
rs28693487	0.97[EUR][1000 genomes]
rs28811645	0.94[ASN][1000 genomes]
rs3760019	0.95[EUR][1000 genomes]
rs3785147	0.97[EUR][1000 genomes]
rs747107	0.95[CHB][hapmap]
rs9937434	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906673	chr16:55631035-55798370	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv431501	chr16:55639454-55789570	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2758426	chr16:55669396-55983590	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2758649	chr16:55669396-55983590	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13333066	SLC6A2	cis	Skin Sun Exposed Lower leg	GTEx
rs13333066	CNGB1	cis	cerebellum	SCAN
rs13333066	GNAO1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:55692600-55705400	Enhancers	Placenta	Placenta
2	chr16:55695600-55703800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr16:55701000-55703600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:55701400-55703600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:55701400-55703600	Enhancers	HMEC	breast
6	chr16:55701600-55703600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr16:55701800-55703200	Enhancers	HepG2	liver
8	chr16:55701800-55703400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:55701800-55703600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr16:55701800-55703600	Enhancers	H9 Cell Line	embryonic stem cell
11	chr16:55702000-55703200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr16:55702000-55703200	Enhancers	Hela-S3	cervix
13	chr16:55702000-55703600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr16:55702000-55703600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr16:55702800-55705600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr16:55703000-55703400	Weak transcription	Fetal Muscle Leg	muscle
17	chr16:55703000-55703800	Enhancers	NHEK	skin
18	chr16:55703000-55706000	Weak transcription	Adipose Nuclei	Adipose
19	chr16:55703000-55731800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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