Variant report

Variant	rs17741233
Chromosome Location	chr5:58828674-58828675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10514860	0.83[CEU][hapmap];1.00[JPT][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]
rs11949561	0.83[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187079	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]
rs12187448	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17728654	1.00[JPT][hapmap]
rs17740749	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740767	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795596	1.00[JPT][hapmap]
rs17795692	1.00[JPT][hapmap]
rs17796040	1.00[JPT][hapmap]
rs17796824	0.83[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797601	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081093	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098699	1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4326095	0.83[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551023	0.83[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075449	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56396168	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861969	1.00[JPT][hapmap]
rs72767794	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767801	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72769704	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[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
rs17741233	PDE4D	cis	parietal	SCAN
rs17741233	SLC38A9	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58815400-58830400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:58819000-58832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:58820000-58831400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:58822200-58838800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:58822800-58837600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:58823000-58838200	Weak transcription	Fetal Brain Male	brain
7	chr5:58824200-58831400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:58824200-58834600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:58824800-58829200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:58824800-58836000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:58825000-58838600	Weak transcription	HSMMtube	muscle
12	chr5:58825400-58830400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:58828200-58836200	Genic enhancers	A549	lung
14	chr5:58828600-58828800	Enhancers	Psoas Muscle	Psoas
15	chr5:58828600-58829000	Enhancers	Brain Hippocampus Middle	brain
16	chr5:58828600-58829600	Enhancers	Brain Substantia Nigra	brain
17	chr5:58828600-58830400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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