Variant report

Variant	rs3791679
Chromosome Location	chr2:56096892-56096893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:56088294..56090507-chr2:56095007..56097587,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10496051	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs11125602	0.93[AMR][1000 genomes]
rs11125606	0.87[AMR][1000 genomes]
rs12464737	0.90[AMR][1000 genomes]
rs12615158	0.89[AMR][1000 genomes]
rs1346786	0.83[CEU][hapmap]
rs1346789	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1430202	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17047234	0.81[AMR][1000 genomes]
rs17369648	0.88[AMR][1000 genomes]
rs1946545	0.90[AMR][1000 genomes]
rs1985163	0.92[AMR][1000 genomes]
rs2009262	0.88[AMR][1000 genomes]
rs3791675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4146921	0.90[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4146922	0.90[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4347871	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58027672	0.88[AMR][1000 genomes]
rs58680090	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59556444	0.86[AMR][1000 genomes]
rs59985551	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62164463	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62167713	0.89[AMR][1000 genomes]
rs6724369	0.90[AMR][1000 genomes]
rs7560657	0.90[AMR][1000 genomes]
rs7563032	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7591694	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Height	20189936	GWAS catalog
Height	23563607	GWAS catalog
Height	18391951	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3791679	EFEMP1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56089200-56097000	Weak transcription	Lung	lung
2	chr2:56089200-56112200	Weak transcription	Pancreas	Pancrea
3	chr2:56089400-56097000	Weak transcription	Right Atrium	heart
4	chr2:56089600-56097000	Weak transcription	HSMMtube	muscle
5	chr2:56089800-56098000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:56090000-56107600	Weak transcription	Fetal Stomach	stomach
7	chr2:56090200-56107400	Weak transcription	Fetal Lung	lung
8	chr2:56091200-56102600	Weak transcription	Hela-S3	cervix
9	chr2:56092000-56099200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:56092400-56100000	Genic enhancers	Osteobl	bone
11	chr2:56092400-56111600	Genic enhancers	HUVEC	blood vessel
12	chr2:56092600-56102600	Strong transcription	HSMM	muscle
13	chr2:56092800-56107800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:56092800-56112400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:56092800-56114400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:56093000-56097200	Weak transcription	NH-A	brain
17	chr2:56093000-56097600	Weak transcription	NHLF	lung
18	chr2:56093000-56098600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:56093800-56109000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:56094800-56116200	Weak transcription	Spleen	Spleen
21	chr2:56095000-56102600	Weak transcription	A549	lung
22	chr2:56095200-56097600	Weak transcription	Placenta	Placenta
23	chr2:56095400-56097000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:56095600-56097000	Weak transcription	Adipose Nuclei	Adipose
25	chr2:56095600-56097000	Weak transcription	NHDF-Ad	bronchial
26	chr2:56095600-56097600	Weak transcription	Aorta	Aorta
27	chr2:56095600-56109600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:56095800-56097000	Weak transcription	HMEC	breast
29	chr2:56096000-56097600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:56096000-56106000	Weak transcription	Ovary	ovary
31	chr2:56096200-56097000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:56096200-56097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:56096200-56097400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:56096600-56097800	Genic enhancers	NHEK	skin
35	chr2:56096800-56097200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:56096800-56097400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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