Variant report

Variant	rs7717808
Chromosome Location	chr5:56994483-56994484
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10057804	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189365	0.81[ASN][1000 genomes]
rs12523004	0.81[EUR][1000 genomes]
rs12652479	0.83[CHD][hapmap]
rs12654040	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654351	1.00[ASN][1000 genomes]
rs12654963	0.81[ASN][1000 genomes]
rs12655658	0.98[ASN][1000 genomes]
rs12658940	1.00[ASN][1000 genomes]
rs13176491	0.83[AFR][1000 genomes]
rs16887298	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215419	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2898027	0.81[EUR][1000 genomes]
rs58041565	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58266257	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59516621	0.91[ASN][1000 genomes]
rs59697426	0.81[ASN][1000 genomes]
rs61220614	0.91[ASN][1000 genomes]
rs62361169	0.81[EUR][1000 genomes]
rs6860385	0.85[AFR][1000 genomes]
rs6862527	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6894116	0.81[EUR][1000 genomes]
rs73089817	1.00[ASN][1000 genomes]
rs73089845	0.85[ASN][1000 genomes]
rs73089868	0.81[ASN][1000 genomes]
rs73089872	0.81[ASN][1000 genomes]
rs73089877	0.81[ASN][1000 genomes]
rs7713500	0.83[CHD][hapmap]
rs7714714	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729312	0.83[CHD][hapmap]
rs7734079	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734787	0.83[CHD][hapmap]
rs978225	0.81[AFR][1000 genomes]

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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7717808	PDE4D	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56987400-56994800	Weak transcription	Right Ventricle	heart
2	chr5:56988600-56995400	Enhancers	Adipose Nuclei	Adipose
3	chr5:56989400-56996000	Enhancers	Fetal Heart	heart
4	chr5:56989600-56994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:56989600-56996400	Weak transcription	Psoas Muscle	Psoas
6	chr5:56990000-56995200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:56990200-57005600	Weak transcription	NH-A	brain
8	chr5:56990400-56996200	Enhancers	HMEC	breast
9	chr5:56990600-56995000	Enhancers	Ovary	ovary
10	chr5:56990600-56996600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:56991400-56995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:56991400-56996000	Enhancers	NHEK	skin
13	chr5:56991600-56994600	Weak transcription	Aorta	Aorta
14	chr5:56992000-56995600	Enhancers	HUVEC	blood vessel
15	chr5:56992200-56994800	Weak transcription	Right Atrium	heart
16	chr5:56992200-56996800	Enhancers	Fetal Lung	lung
17	chr5:56992400-56995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:56992400-56995400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:56992400-56995400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:56992400-57004400	Weak transcription	Left Ventricle	heart
21	chr5:56992800-56995000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:56993000-56994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:56993000-56994800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:56993200-56994600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:56993400-56994600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:56993600-56994800	Enhancers	HSMM	muscle
27	chr5:56993600-56995200	Enhancers	A549	lung
28	chr5:56993600-56995400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr5:56993800-56994600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:56993800-56994800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:56994000-56994800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr5:56994200-56994600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:56994200-56994600	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:56994200-56994800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:56994200-56995400	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr5:56994200-56995600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:56994200-56996000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr5:56994200-56996000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:56994400-56994800	Enhancers	Stomach Smooth Muscle	stomach

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