Variant report

Variant	rs12187079
Chromosome Location	chr5:58823366-58823367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10514860	1.00[CEU][hapmap];1.00[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]
rs11949561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187448	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17728654	1.00[JPT][hapmap]
rs17740749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740767	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741233	0.83[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795596	1.00[JPT][hapmap]
rs17795692	1.00[JPT][hapmap]
rs17796040	1.00[JPT][hapmap]
rs17796824	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797601	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081093	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098699	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4326095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551023	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075449	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56396168	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861969	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs72767794	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767801	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767802	0.84[EUR][1000 genomes]
rs72769704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717821	1.00[JPT][hapmap]
rs7729912	1.00[JPT][hapmap]
rs7737908	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12187079	PDE4D	cis	parietal	SCAN
rs12187079	SLC38A9	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58810000-58823600	Weak transcription	Colon Smooth Muscle	Colon
2	chr5:58814600-58823800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:58815400-58830400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:58815800-58823600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:58818800-58823800	Weak transcription	Stomach Mucosa	stomach
6	chr5:58819000-58832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:58820000-58831400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:58820800-58824600	Weak transcription	Psoas Muscle	Psoas
9	chr5:58821000-58828600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:58821600-58823800	Weak transcription	Brain Substantia Nigra	brain
11	chr5:58822200-58824000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:58822200-58838800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:58822400-58823800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:58822400-58823800	Enhancers	A549	lung
15	chr5:58822600-58823600	Weak transcription	NH-A	brain
16	chr5:58822600-58823800	Weak transcription	HSMM	muscle
17	chr5:58822600-58824000	Weak transcription	Fetal Intestine Small	intestine
18	chr5:58822600-58824400	Weak transcription	HSMMtube	muscle
19	chr5:58822800-58824200	Weak transcription	Fetal Intestine Large	intestine
20	chr5:58822800-58824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:58822800-58837600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:58823000-58823400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:58823000-58823400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:58823000-58823600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:58823000-58838200	Weak transcription	Fetal Brain Male	brain
26	chr5:58823200-58823600	Weak transcription	HUVEC	blood vessel
27	chr5:58823200-58824000	Weak transcription	Duodenum Mucosa	Duodenum

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