Variant report

Variant	rs4700328
Chromosome Location	chr5:58562465-58562466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1031197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10491352	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940644	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11954668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11959132	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11959567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12189022	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518773	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12519611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12521263	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12522944	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1445948	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1445952	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1445954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1579848	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1579849	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16889479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889499	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889518	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444185	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17528522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528578	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17780175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1823070	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1838733	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1840846	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867712	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1947090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947095	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013979	0.81[CHD][hapmap]
rs2021775	1.00[JPT][hapmap]
rs2028836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4700325	1.00[JPT][hapmap]
rs6858946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6877508	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888028	0.81[ASN][1000 genomes]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7443333	0.93[GIH][hapmap]
rs7703022	1.00[CHB][hapmap]
rs7717303	0.81[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4700328	PLK2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:58553800-58568600	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:58554200-58562600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:58558400-58564400	Enhancers	Fetal Heart	heart
5	chr5:58559200-58564200	Weak transcription	Pancreas	Pancrea
6	chr5:58560200-58566600	Enhancers	Rectal Smooth Muscle	rectum
7	chr5:58560400-58570000	Weak transcription	Fetal Lung	lung
8	chr5:58560600-58563800	Enhancers	Fetal Intestine Large	intestine
9	chr5:58561000-58562600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:58561000-58563200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr5:58561000-58569800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:58561000-58571000	Weak transcription	Left Ventricle	heart
13	chr5:58561400-58563200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:58561600-58562800	Enhancers	Stomach Mucosa	stomach
15	chr5:58561600-58563200	Enhancers	Fetal Intestine Small	intestine
16	chr5:58562000-58565400	Enhancers	Colon Smooth Muscle	Colon
17	chr5:58562200-58562800	Active TSS	Hela-S3	cervix
18	chr5:58562200-58562800	Enhancers	HepG2	liver
19	chr5:58562200-58563000	Enhancers	Psoas Muscle	Psoas
20	chr5:58562200-58564000	Flanking Active TSS	A549	lung
21	chr5:58562400-58562600	Enhancers	Colonic Mucosa	Colon
22	chr5:58562400-58563000	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr5:58562400-58563000	Enhancers	Rectal Mucosa Donor 29	rectum

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