Variant report

Variant	rs13179321
Chromosome Location	chr5:59027953-59027954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11738977	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11739906	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11954036	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.95[ASN][1000 genomes]
rs13171758	0.92[ASN][1000 genomes]
rs17742447	0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs17799191	1.00[ASN][1000 genomes]
rs297975	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs298060	0.90[CHD][hapmap]
rs298064	0.90[CHD][hapmap]
rs298068	0.85[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs298071	0.80[ASN][1000 genomes]
rs298073	0.80[ASN][1000 genomes]
rs298079	0.83[ASN][1000 genomes]
rs298085	0.83[ASN][1000 genomes]
rs298086	0.80[ASN][1000 genomes]
rs298088	0.81[ASN][1000 genomes]
rs298089	0.81[ASN][1000 genomes]
rs298090	0.81[ASN][1000 genomes]
rs298094	0.84[ASN][1000 genomes]
rs298095	0.81[ASN][1000 genomes]
rs298098	0.85[ASN][1000 genomes]
rs298100	0.87[ASN][1000 genomes]
rs298101	0.89[CHD][hapmap];0.87[ASN][1000 genomes]
rs298102	0.87[ASN][1000 genomes]
rs34032696	0.94[ASN][1000 genomes]
rs6877662	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746477	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs7700279	1.00[ASN][1000 genomes]
rs7702956	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7711313	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720119	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs893191	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1034283	chr5:58940594-59040762	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv537767	chr5:58940594-59040762	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	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
8	nsv462191	chr5:58993297-59038610	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv598259	chr5:58993297-59038610	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13179321	Contig33579_RC	cis	multi-tissue	Pritchard
rs13179321	PDE4D	cis	Liver	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59017800-59028400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:59021200-59040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:59022200-59030200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:59023000-59028000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:59023000-59029600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr5:59025400-59028400	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:59025400-59028800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:59026200-59029000	Weak transcription	Aorta	Aorta
9	chr5:59026400-59029600	Enhancers	A549	lung
10	chr5:59026600-59028600	Weak transcription	Hela-S3	cervix
11	chr5:59027000-59028000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:59027000-59029000	Enhancers	Fetal Lung	lung
13	chr5:59027200-59029200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:59027400-59028800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:59027600-59028400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr5:59027600-59029000	Enhancers	Brain Substantia Nigra	brain
17	chr5:59027800-59028400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:59027800-59028600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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