Variant report

No.	Distal block	Cell Line	Cell type
1	chr1:223585376..223587984-chr1:223593733..223596236,2	MCF-7	breast:
2	chr1:223566045..223568415-chr1:223593690..223595373,2	MCF-7	breast:
3	chr1:223594003..223597385-chr1:223616098..223619072,3	MCF-7	breast:
4	chr1:223566366..223568039-chr1:223593781..223595649,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178395	Chromatin interaction

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10494039	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10495206	0.84[JPT][hapmap]
rs10495207	0.92[JPT][hapmap]
rs10907376	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1115114	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11261264	0.92[JPT][hapmap]
rs11261270	0.80[AMR][1000 genomes]
rs11590684	1.00[CHB][hapmap];0.92[MEX][hapmap]
rs12123148	0.92[JPT][hapmap]
rs12134824	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140453	0.92[JPT][hapmap];0.86[MEX][hapmap]
rs12141995	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12564615	0.92[JPT][hapmap]
rs1400959	0.84[JPT][hapmap]
rs17480087	0.84[JPT][hapmap]
rs17480344	0.92[JPT][hapmap]
rs17518349	0.84[JPT][hapmap]
rs17518363	0.84[JPT][hapmap]
rs17539269	0.84[JPT][hapmap]
rs17539583	0.92[JPT][hapmap]
rs17578168	0.92[JPT][hapmap]
rs17578203	0.92[JPT][hapmap]
rs2138966	0.81[AMR][1000 genomes]
rs2176507	0.85[TSI][hapmap]
rs59355120	0.81[AMR][1000 genomes]
rs61839876	0.81[AMR][1000 genomes]
rs61839877	0.81[AMR][1000 genomes]
rs61839879	0.81[AMR][1000 genomes]
rs61839881	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526539	0.87[AMR][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	nsv832670	chr1:223561771-223683381	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv4687	chr1:223565080-223610362	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17162072	SUSD4	cis	cerebellum	SCAN
rs17162072	SUSD4	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223591200-223595200	Enhancers	Pancreas	Pancrea
2	chr1:223592400-223596000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:223592600-223595200	Enhancers	Fetal Heart	heart
4	chr1:223592600-223597400	Weak transcription	Right Ventricle	heart
5	chr1:223593600-223595200	Enhancers	Gastric	stomach
6	chr1:223594200-223595000	Enhancers	Liver	Liver
7	chr1:223594400-223595000	Enhancers	Left Ventricle	heart
8	chr1:223594400-223595200	Enhancers	Stomach Mucosa	stomach
9	chr1:223594400-223595600	Enhancers	HMEC	breast
10	chr1:223594600-223595000	Enhancers	Ovary	ovary
11	chr1:223594600-223595200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:223594600-223595200	Enhancers	Esophagus	oesophagus
13	chr1:223594600-223595200	Enhancers	Placenta	Placenta
14	chr1:223594600-223595200	Enhancers	Right Atrium	heart
15	chr1:223594600-223595800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:223594600-223595800	Enhancers	NHEK	skin
17	chr1:223594600-223596000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:223594600-223597800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:223594800-223595200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:223594800-223595200	Enhancers	Lung	lung
21	chr1:223594800-223596400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:223594800-223600600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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