Variant report

Variant	rs2028836
Chromosome Location	chr5:58583213-58583214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1031197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10491352	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10940644	0.80[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs11744761	0.87[ASN][1000 genomes]
rs11954668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11959132	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11959567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12189022	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12518773	0.83[ASN][1000 genomes]
rs12519611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521263	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522944	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1445948	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445952	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1445953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1445954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1579848	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579849	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16889499	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16889518	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17444185	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17528522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17528578	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17780175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1823070	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1838733	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1840846	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1867711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867712	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1947090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1947095	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2021775	1.00[JPT][hapmap]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4700325	1.00[JPT][hapmap]
rs4700328	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]
rs6858946	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6877508	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][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]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7443333	0.93[GIH][hapmap]
rs7703022	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

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	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
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2028836	PLK2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58573400-58583400	Weak transcription	Colon Smooth Muscle	Colon
2	chr5:58574200-58590200	Weak transcription	Right Atrium	heart
3	chr5:58582400-58587000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:58582800-58583600	Enhancers	Psoas Muscle	Psoas
5	chr5:58582800-58583800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:58582800-58584000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr5:58582800-58584200	Enhancers	HUVEC	blood vessel
8	chr5:58583000-58583400	Enhancers	Lung	lung
9	chr5:58583000-58583600	Enhancers	Left Ventricle	heart
10	chr5:58583000-58583600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr5:58583000-58583600	Enhancers	Spleen	Spleen
12	chr5:58583000-58583800	Enhancers	Right Ventricle	heart
13	chr5:58583000-58584000	Enhancers	Gastric	stomach
14	chr5:58583000-58584000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr5:58583000-58584000	Enhancers	Rectal Smooth Muscle	rectum
16	chr5:58583000-58584000	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr5:58583000-58584200	Enhancers	Fetal Heart	heart
18	chr5:58583000-58584800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:58583200-58583400	Flanking Active TSS	Hela-S3	cervix
20	chr5:58583200-58583600	Enhancers	Esophagus	oesophagus
21	chr5:58583200-58584000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:58583200-58584000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:58583200-58584000	Flanking Active TSS	A549	lung
24	chr5:58583200-58584000	Enhancers	HMEC	breast

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