Variant report

Variant	rs17444059
Chromosome Location	chr5:58560717-58560718
allele	C/T
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:40)

rs_ID	r²[population]
rs10036406	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs10038599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10055446	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10056754	1.00[LWK][hapmap]
rs10059709	0.88[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap]
rs10061600	0.83[ASN][1000 genomes]
rs10061786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062176	1.00[LWK][hapmap]
rs10064893	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.87[ASN][1000 genomes]
rs10068836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10070294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070436	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10075364	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10440630	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs11740402	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11747413	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13328160	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13328175	0.83[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13328226	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13354210	0.84[CEU][hapmap]
rs13360907	0.98[ASN][1000 genomes]
rs17528257	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17528285	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.87[ASN][1000 genomes]
rs17528473	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528634	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17780213	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap]
rs17780740	0.83[CEU][hapmap]
rs2112959	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529077	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647633	0.98[ASN][1000 genomes]
rs60453299	0.98[ASN][1000 genomes]
rs61683381	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6881054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765932	0.87[ASN][1000 genomes]
rs72765942	0.98[ASN][1000 genomes]
rs72765953	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765990	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9292201	0.84[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs9686434	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Immune response to smallpox vaccine (IL-6)	22610502	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17444059	PLK2	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58553800-58568600	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:58554200-58561000	Weak transcription	Stomach Mucosa	stomach
5	chr5:58554200-58562600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:58557200-58562400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:58558000-58561000	Weak transcription	Fetal Intestine Small	intestine
8	chr5:58558400-58564400	Enhancers	Fetal Heart	heart
9	chr5:58558600-58561000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:58559200-58561000	Enhancers	Hela-S3	cervix
11	chr5:58559200-58562200	Weak transcription	Psoas Muscle	Psoas
12	chr5:58559200-58564200	Weak transcription	Pancreas	Pancrea
13	chr5:58559400-58561400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:58559600-58560800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:58559800-58561800	Flanking Active TSS	A549	lung
16	chr5:58559800-58562400	Weak transcription	Colonic Mucosa	Colon
17	chr5:58560000-58561000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:58560000-58561200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr5:58560000-58561200	Enhancers	HSMMtube	muscle
20	chr5:58560200-58561000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:58560200-58561800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr5:58560200-58566600	Enhancers	Rectal Smooth Muscle	rectum
23	chr5:58560400-58560800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:58560400-58561000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr5:58560400-58561000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr5:58560400-58561200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr5:58560400-58570000	Weak transcription	Fetal Lung	lung
28	chr5:58560600-58560800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:58560600-58560800	Enhancers	Fetal Kidney	kidney
30	chr5:58560600-58561000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr5:58560600-58561000	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr5:58560600-58561000	Enhancers	Left Ventricle	heart
33	chr5:58560600-58561000	Enhancers	Right Atrium	heart
34	chr5:58560600-58561000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr5:58560600-58561200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:58560600-58561200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr5:58560600-58561200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:58560600-58561400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:58560600-58563800	Enhancers	Fetal Intestine Large	intestine

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