Variant report

Variant	rs1544621
Chromosome Location	chr5:57065117-57065118
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:57064652..57067649-chr5:57101183..57103677,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10447121	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10940574	0.81[EUR][1000 genomes]
rs10940578	0.87[EUR][1000 genomes]
rs12186536	0.87[EUR][1000 genomes]
rs12514617	0.81[EUR][1000 genomes]
rs12514618	0.81[EUR][1000 genomes]
rs12515493	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12515736	0.82[EUR][1000 genomes]
rs12517238	0.90[EUR][1000 genomes]
rs12517867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12520466	0.80[EUR][1000 genomes]
rs12522697	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1432482	0.86[EUR][1000 genomes]
rs17689645	0.80[EUR][1000 genomes]
rs17689832	0.82[EUR][1000 genomes]
rs17690351	0.90[EUR][1000 genomes]
rs17690411	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs17746879	0.90[EUR][1000 genomes]
rs17746968	0.84[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2160057	0.82[EUR][1000 genomes]
rs2160058	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2192367	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2192368	0.82[EUR][1000 genomes]
rs56830694	0.87[EUR][1000 genomes]
rs57200729	0.90[EUR][1000 genomes]
rs58610852	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58632739	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62358372	0.81[EUR][1000 genomes]
rs62358374	0.81[EUR][1000 genomes]
rs62358380	0.82[EUR][1000 genomes]
rs62358381	0.83[EUR][1000 genomes]
rs6450432	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450433	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450434	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450435	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450437	0.93[EUR][1000 genomes]
rs6870485	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6878042	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs6891648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6894375	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs72751313	0.90[EUR][1000 genomes]
rs72751317	0.90[EUR][1000 genomes]
rs72751318	0.90[EUR][1000 genomes]
rs72751323	0.88[EUR][1000 genomes]
rs72767430	0.80[EUR][1000 genomes]
rs72767434	0.82[EUR][1000 genomes]
rs72767441	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72767444	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs741181	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7718447	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs1544621	PDE4D	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57056400-57065200	Weak transcription	Aorta	Aorta
2	chr5:57062200-57075000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:57064200-57065400	Enhancers	Adipose Nuclei	Adipose
4	chr5:57064200-57065400	Enhancers	NHLF	lung
5	chr5:57064200-57065600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:57064400-57065200	Enhancers	Osteobl	bone
7	chr5:57064400-57065400	Enhancers	Fetal Lung	lung
8	chr5:57064600-57065200	Enhancers	NHDF-Ad	bronchial
9	chr5:57064800-57065600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:57064800-57068400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:57065000-57065400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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