Variant report

Variant	rs1838733
Chromosome Location	chr5:58533392-58533393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58532712..58534586-chr5:58538179..58539997,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1031197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10491352	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10940644	1.00[JPT][hapmap]
rs11954668	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11959132	1.00[JPT][hapmap]
rs11959567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs12519611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445948	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1445953	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445954	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1471429	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471430	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889479	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17444185	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17528522	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17780175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1824157	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1867711	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1947090	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2021775	1.00[JPT][hapmap]
rs2028836	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28862729	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700325	1.00[JPT][hapmap]
rs4700327	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4700328	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs67196739	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67526430	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6877508	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6888028	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6897568	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765182	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7703022	1.00[CHB][hapmap]
rs7717303	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1023570	chr5:58486384-58537849	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	nsv881703	chr5:58517918-58540847	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1025807	chr5:58520050-58548231	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv520721	chr5:58520735-58558388	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1838733	PLK2	cis	parietal	SCAN
rs1838733	ELOVL7	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58519200-58535000	Weak transcription	Left Ventricle	heart
2	chr5:58520800-58537000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58527400-58549800	Weak transcription	Aorta	Aorta
4	chr5:58529600-58533400	Enhancers	Fetal Heart	heart
5	chr5:58529800-58535000	Weak transcription	Right Atrium	heart
6	chr5:58531000-58537600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr5:58531200-58534600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:58531600-58533400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:58531800-58535600	Enhancers	HUVEC	blood vessel
10	chr5:58532000-58534000	Enhancers	Right Ventricle	heart
11	chr5:58532200-58533400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:58532200-58533600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:58532200-58533800	Flanking Active TSS	A549	lung
14	chr5:58532600-58533600	Weak transcription	Psoas Muscle	Psoas
15	chr5:58532600-58540800	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:58532600-58541000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:58532800-58533800	Enhancers	Hela-S3	cervix
18	chr5:58533000-58535200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:58533200-58534400	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:58533200-58536800	Weak transcription	Osteobl	bone
21	chr5:58533200-58540800	Weak transcription	HSMMtube	muscle

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