Variant report

Variant	rs1504982
Chromosome Location	chr5:59065790-59065791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:59065696-59066058	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr5:59065372-59066030	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr5:59063629-59065972	MCF10A-Er-Src	breast:	n/a	chr5:59064369-59064378
4	FOS	chr5:59065534-59066104	MCF10A-Er-Src	breast:	n/a	chr5:59065749-59065758
5	STAT3	chr5:59065686-59066028	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr5:59060956-59066265	MCF10A-Er-Src	breast:	n/a	n/a
7	TBP	chr5:59062014-59066021	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:59059243-59065851	Hela-S3	cervix:	n/a	n/a
9	MYC	chr5:59065438-59065893	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr5:59065709-59066125	HUVEC	blood vessel:	n/a	chr5:59065749-59065758
11	POLR2A	chr5:59060717-59070261	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr5:59065776-59066040	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr5:59065721-59066063	MCF10A-Er-Src	breast:	n/a	chr5:59065749-59065758

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10043265	0.96[ASN][1000 genomes]
rs10043283	0.96[ASN][1000 genomes]
rs1027747	0.92[EUR][1000 genomes]
rs10514857	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11949859	0.84[ASN][1000 genomes]
rs12187752	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12188131	0.88[ASN][1000 genomes]
rs13155799	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13168347	0.93[EUR][1000 genomes]
rs1362941	0.88[ASN][1000 genomes]
rs1362942	0.88[ASN][1000 genomes]
rs1437124	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1504984	0.90[ASN][1000 genomes]
rs16877195	0.88[ASN][1000 genomes]
rs17369708	0.93[ASN][1000 genomes]
rs17381695	0.81[ASN][1000 genomes]
rs17381723	0.81[ASN][1000 genomes]
rs17382202	0.84[ASN][1000 genomes]
rs17441217	0.81[ASN][1000 genomes]
rs17441825	0.84[ASN][1000 genomes]
rs17742120	0.85[ASN][1000 genomes]
rs17742544	0.88[ASN][1000 genomes]
rs17743216	0.88[ASN][1000 genomes]
rs17799161	0.88[ASN][1000 genomes]
rs2164660	0.88[ASN][1000 genomes]
rs28583502	0.93[ASN][1000 genomes]
rs2938780	0.87[EUR][1000 genomes]
rs2963826	0.87[EUR][1000 genomes]
rs36143327	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3898713	0.91[ASN][1000 genomes]
rs4577665	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699942	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699943	0.88[ASN][1000 genomes]
rs4700340	0.88[ASN][1000 genomes]
rs4700341	0.96[ASN][1000 genomes]
rs4700342	0.91[EUR][1000 genomes]
rs55704150	0.93[ASN][1000 genomes]
rs55868825	0.88[ASN][1000 genomes]
rs56199003	0.88[ASN][1000 genomes]
rs6450528	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6450530	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860907	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874708	0.96[ASN][1000 genomes]
rs6889294	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6897073	0.88[ASN][1000 genomes]
rs72751211	0.84[ASN][1000 genomes]
rs72751218	0.84[ASN][1000 genomes]
rs72751226	0.85[ASN][1000 genomes]
rs72751229	0.88[ASN][1000 genomes]
rs72751231	0.88[ASN][1000 genomes]
rs72751232	0.88[ASN][1000 genomes]
rs72751233	0.88[ASN][1000 genomes]
rs72751234	0.88[ASN][1000 genomes]
rs72751235	0.88[ASN][1000 genomes]
rs72751237	0.88[ASN][1000 genomes]
rs72751241	0.88[ASN][1000 genomes]
rs72751244	0.88[ASN][1000 genomes]
rs72751247	0.88[ASN][1000 genomes]
rs72751250	0.88[ASN][1000 genomes]
rs72751252	0.91[ASN][1000 genomes]
rs72751264	0.88[ASN][1000 genomes]
rs756211	0.93[ASN][1000 genomes]
rs756212	0.93[ASN][1000 genomes]
rs7708952	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710199	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7736817	0.94[ASN][1000 genomes]
rs877745	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981230	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59063000-59065800	Active TSS	HMEC	breast
2	chr5:59064800-59067600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:59064800-59067800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:59065000-59065800	Enhancers	HSMM	muscle
5	chr5:59065200-59065800	Enhancers	HepG2	liver
6	chr5:59065200-59066000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:59065200-59066000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:59065200-59066000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr5:59065200-59066000	Flanking Active TSS	A549	lung
10	chr5:59065200-59066200	Enhancers	NH-A	brain
11	chr5:59065200-59066400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:59065200-59067600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:59065200-59068000	Weak transcription	Stomach Mucosa	stomach
14	chr5:59065200-59072800	Weak transcription	Aorta	Aorta
15	chr5:59065400-59065800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:59065400-59065800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:59065400-59065800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:59065400-59066000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:59065400-59066000	Flanking Active TSS	NHEK	skin
20	chr5:59065400-59066400	Enhancers	HUVEC	blood vessel
21	chr5:59065600-59065800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr5:59065600-59065800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:59065600-59066000	Flanking Active TSS	Hela-S3	cervix
24	chr5:59065600-59067400	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:59065600-59067400	Weak transcription	Rectal Smooth Muscle	rectum

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