Variant report

Variant	rs10043283
Chromosome Location	chr5:59042867-59042868
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	chr5:59042416..59043177-chr6:10415490..10415996,2	Hela-S3	cervix:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10043265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514857	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10940649	1.00[YRI][hapmap]
rs11949859	0.89[ASN][1000 genomes]
rs12152908	0.83[ASN][1000 genomes]
rs12187752	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs12188131	0.93[ASN][1000 genomes]
rs13155799	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1362941	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs1362942	0.93[ASN][1000 genomes]
rs1437124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1504982	0.96[ASN][1000 genomes]
rs1504984	0.86[ASN][1000 genomes]
rs16877195	0.83[CHB][hapmap];0.86[CHD][hapmap];0.93[ASN][1000 genomes]
rs17311853	1.00[YRI][hapmap]
rs17311925	1.00[YRI][hapmap]
rs17369708	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs17371174	1.00[YRI][hapmap]
rs17381667	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs17381695	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs17381723	0.86[ASN][1000 genomes]
rs17382202	0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[ASN][1000 genomes]
rs17440909	0.83[CHB][hapmap]
rs17441217	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs17441825	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs17742120	0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[ASN][1000 genomes]
rs17742544	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[ASN][1000 genomes]
rs17743216	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs17799161	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs2164660	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs28583502	0.89[ASN][1000 genomes]
rs3898713	0.83[CHB][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs4577665	0.96[ASN][1000 genomes]
rs4699942	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs4699943	0.83[CHB][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs4700340	0.83[CHB][hapmap];0.81[CHD][hapmap];0.93[ASN][1000 genomes]
rs4700341	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55704150	0.89[ASN][1000 genomes]
rs55868825	0.93[ASN][1000 genomes]
rs56199003	0.93[ASN][1000 genomes]
rs6450528	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6450530	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs6860907	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs6874708	1.00[ASN][1000 genomes]
rs6889294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6897073	0.83[CHB][hapmap];0.86[CHD][hapmap];0.93[ASN][1000 genomes]
rs72751211	0.89[ASN][1000 genomes]
rs72751218	0.89[ASN][1000 genomes]
rs72751226	0.90[ASN][1000 genomes]
rs72751229	0.93[ASN][1000 genomes]
rs72751231	0.93[ASN][1000 genomes]
rs72751232	0.93[ASN][1000 genomes]
rs72751233	0.93[ASN][1000 genomes]
rs72751234	0.93[ASN][1000 genomes]
rs72751235	0.93[ASN][1000 genomes]
rs72751237	0.93[ASN][1000 genomes]
rs72751241	0.93[ASN][1000 genomes]
rs72751244	0.93[ASN][1000 genomes]
rs72751247	0.93[ASN][1000 genomes]
rs72751250	0.93[ASN][1000 genomes]
rs72751252	0.90[ASN][1000 genomes]
rs72751264	0.84[ASN][1000 genomes]
rs756211	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs756212	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs7703963	1.00[YRI][hapmap]
rs7708952	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs7710199	1.00[ASN][1000 genomes]
rs7732908	0.94[LWK][hapmap]
rs7736817	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs877745	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs981230	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10043283	PDE4D	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59028000-59043200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:59039400-59059800	Weak transcription	Primary B cells from cord blood	blood
3	chr5:59039600-59043000	Enhancers	HUVEC	blood vessel
4	chr5:59040400-59043400	Enhancers	Colon Smooth Muscle	Colon
5	chr5:59041000-59043400	Enhancers	Fetal Brain Male	brain
6	chr5:59041000-59047000	Weak transcription	Fetal Intestine Small	intestine
7	chr5:59041600-59043000	Enhancers	Fetal Lung	lung
8	chr5:59041600-59043000	Enhancers	NHEK	skin
9	chr5:59041600-59046400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:59041600-59049600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:59041600-59052200	Weak transcription	Aorta	Aorta
12	chr5:59041800-59043200	Flanking Active TSS	A549	lung
13	chr5:59042200-59043800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:59042200-59047000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:59042200-59047000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:59042200-59047200	Weak transcription	HSMMtube	muscle
17	chr5:59042200-59047400	Weak transcription	Osteobl	bone
18	chr5:59042400-59053400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:59042600-59043000	Enhancers	Hela-S3	cervix
20	chr5:59042600-59046200	Weak transcription	NH-A	brain
21	chr5:59042600-59046800	Weak transcription	HMEC	breast
22	chr5:59042600-59047000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:59042600-59047000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:59042600-59047200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:59042600-59047200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:59042600-59047200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:59042600-59047400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:59042600-59048000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:59042600-59055400	Weak transcription	Esophagus	oesophagus
30	chr5:59042800-59047000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:59042800-59047000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:59042800-59047000	Weak transcription	HSMM	muscle

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