Variant report

Variant	rs6870485
Chromosome Location	chr5:57041324-57041325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10447121	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10940574	0.83[EUR][1000 genomes]
rs10940578	0.85[EUR][1000 genomes]
rs12186536	0.85[EUR][1000 genomes]
rs12514617	0.83[EUR][1000 genomes]
rs12514618	0.83[EUR][1000 genomes]
rs12515493	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12517238	0.88[EUR][1000 genomes]
rs12517867	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12520466	0.82[EUR][1000 genomes]
rs12522697	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12523004	0.81[EUR][1000 genomes]
rs1432482	0.83[EUR][1000 genomes]
rs1544621	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17689645	0.82[EUR][1000 genomes]
rs17689832	0.85[EUR][1000 genomes]
rs17690351	0.88[EUR][1000 genomes]
rs17690411	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs17746879	0.88[EUR][1000 genomes]
rs17746968	0.84[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs17747913	1.00[CHD][hapmap]
rs2160057	0.85[EUR][1000 genomes]
rs2160058	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2192367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2192368	0.85[EUR][1000 genomes]
rs2898027	0.81[EUR][1000 genomes]
rs56830694	0.85[EUR][1000 genomes]
rs57200729	0.88[EUR][1000 genomes]
rs58610852	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58632739	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62358372	0.83[EUR][1000 genomes]
rs62358374	0.83[EUR][1000 genomes]
rs62358380	0.85[EUR][1000 genomes]
rs62358381	0.86[EUR][1000 genomes]
rs62361169	0.81[EUR][1000 genomes]
rs6450432	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6450433	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6450434	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6450435	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6450437	0.90[EUR][1000 genomes]
rs6872726	1.00[CHD][hapmap]
rs6878042	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs6891648	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6894116	0.81[EUR][1000 genomes]
rs6894375	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs72751313	0.88[EUR][1000 genomes]
rs72751317	0.88[EUR][1000 genomes]
rs72751318	0.88[EUR][1000 genomes]
rs72751323	0.86[EUR][1000 genomes]
rs72767430	0.82[EUR][1000 genomes]
rs72767434	0.85[EUR][1000 genomes]
rs72767441	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72767444	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs741181	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7718447	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][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	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
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6870485	PDE4D	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57033000-57041400	Weak transcription	NH-A	brain
2	chr5:57033000-57044800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:57033400-57041600	Weak transcription	NHDF-Ad	bronchial
4	chr5:57034200-57042200	Weak transcription	Fetal Kidney	kidney
5	chr5:57037400-57041600	Weak transcription	Osteobl	bone
6	chr5:57037800-57041400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:57037800-57045000	Weak transcription	HMEC	breast
8	chr5:57038600-57042600	Weak transcription	Hela-S3	cervix
9	chr5:57040200-57041800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:57040200-57042600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:57040400-57042400	Enhancers	Brain Germinal Matrix	brain
12	chr5:57040600-57042000	Enhancers	NHLF	lung
13	chr5:57040600-57042600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:57041000-57041600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr5:57041000-57041800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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