Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:238593632..238594527-chr4:152881866..152882771,2	MCF-7	breast:

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10517559	0.86[YRI][hapmap]
rs1531917	0.86[YRI][hapmap]
rs165579	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs171507	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1872314	0.88[YRI][hapmap]
rs360913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360914	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs360916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360917	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs360931	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs360932	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs360950	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360951	0.85[GIH][hapmap]
rs360953	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs361147	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs361148	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs361149	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6535830	0.89[YRI][hapmap]
rs975820	0.83[YRI][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	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs360954	FGA	cis	parietal	SCAN
rs360954	NR3C2	cis	parietal	SCAN
rs360954	FBXW7	cis	parietal	SCAN
rs360954	FGG	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152877400-152883800	Enhancers	Fetal Heart	heart
2	chr4:152878000-152883000	Weak transcription	Brain Angular Gyrus	brain
3	chr4:152878800-152882800	Weak transcription	Ovary	ovary
4	chr4:152878800-152883000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:152879000-152886400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:152880400-152883600	Enhancers	Fetal Brain Male	brain
7	chr4:152881000-152883200	Enhancers	HSMMtube	muscle
8	chr4:152881200-152882800	Enhancers	Fetal Muscle Leg	muscle
9	chr4:152881800-152882800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:152881800-152884000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:152882000-152882800	Enhancers	Fetal Brain Female	brain
12	chr4:152882000-152882800	Enhancers	HMEC	breast
13	chr4:152882000-152884000	Enhancers	NHEK	skin
14	chr4:152882200-152883400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr4:152882200-152883400	Enhancers	Right Atrium	heart
16	chr4:152882200-152884200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr4:152882400-152882800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:152882400-152883400	Weak transcription	Hela-S3	cervix
19	chr4:152882600-152883000	Enhancers	Psoas Muscle	Psoas
20	chr4:152882600-152883600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:152882600-152884200	Enhancers	Skeletal Muscle Female	skeletal muscle

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