Variant report

Variant	rs16890279
Chromosome Location	chr5:59138714-59138715
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10036621	0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10037195	1.00[EUR][1000 genomes]
rs10070270	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10076058	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10078146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10214307	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10472115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10514882	1.00[EUR][1000 genomes]
rs16890137	1.00[EUR][1000 genomes]
rs16890246	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16890284	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16890314	0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2016004	1.00[EUR][1000 genomes]
rs3797208	1.00[EUR][1000 genomes]
rs4602573	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55641022	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55720412	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55930874	1.00[EUR][1000 genomes]
rs56203004	1.00[EUR][1000 genomes]
rs57153097	1.00[EUR][1000 genomes]
rs57402847	1.00[EUR][1000 genomes]
rs57413746	1.00[EUR][1000 genomes]
rs57434558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57438370	1.00[EUR][1000 genomes]
rs57465219	1.00[EUR][1000 genomes]
rs57742530	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58746465	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58815573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59025824	1.00[EUR][1000 genomes]
rs60774517	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61146095	1.00[EUR][1000 genomes]
rs6450533	1.00[EUR][1000 genomes]
rs6450534	0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861008	1.00[EUR][1000 genomes]
rs6861209	1.00[EUR][1000 genomes]
rs6862255	1.00[EUR][1000 genomes]
rs6866277	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6867150	1.00[EUR][1000 genomes]
rs6869978	1.00[EUR][1000 genomes]
rs6873715	1.00[EUR][1000 genomes]
rs6873774	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6874354	1.00[EUR][1000 genomes]
rs6874831	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6876534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6878243	1.00[EUR][1000 genomes]
rs6882607	1.00[EUR][1000 genomes]
rs6885868	1.00[EUR][1000 genomes]
rs6888341	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6889471	1.00[EUR][1000 genomes]
rs6891000	1.00[EUR][1000 genomes]
rs6893381	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6895425	1.00[EUR][1000 genomes]
rs6896644	1.00[EUR][1000 genomes]
rs6896871	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73092839	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73092846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73758838	1.00[EUR][1000 genomes]
rs73758839	1.00[EUR][1000 genomes]
rs73758847	1.00[EUR][1000 genomes]
rs73758850	1.00[EUR][1000 genomes]
rs73758851	1.00[EUR][1000 genomes]
rs73758856	1.00[EUR][1000 genomes]
rs73758857	1.00[EUR][1000 genomes]
rs73758858	1.00[EUR][1000 genomes]
rs73758859	1.00[EUR][1000 genomes]
rs73758860	1.00[EUR][1000 genomes]
rs73758862	1.00[EUR][1000 genomes]
rs73758864	1.00[EUR][1000 genomes]
rs73758867	1.00[EUR][1000 genomes]
rs73758868	1.00[EUR][1000 genomes]
rs73761012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7703935	1.00[EUR][1000 genomes]
rs7705119	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7705820	1.00[EUR][1000 genomes]
rs7707756	1.00[EUR][1000 genomes]
rs7707855	1.00[EUR][1000 genomes]
rs7708246	1.00[EUR][1000 genomes]
rs7709094	1.00[EUR][1000 genomes]
rs7709292	1.00[EUR][1000 genomes]
rs7710349	1.00[EUR][1000 genomes]
rs7711022	1.00[EUR][1000 genomes]
rs7713509	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7713964	1.00[EUR][1000 genomes]
rs7716837	1.00[EUR][1000 genomes]
rs7718096	0.82[AFR][1000 genomes]
rs7723356	1.00[EUR][1000 genomes]
rs7727677	1.00[EUR][1000 genomes]
rs7728346	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7729112	1.00[EUR][1000 genomes]
rs7729853	1.00[EUR][1000 genomes]
rs7731666	0.82[AFR][1000 genomes]
rs7734202	1.00[EUR][1000 genomes]
rs7737029	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7737211	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292215	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292216	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292217	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9765834	1.00[EUR][1000 genomes]
rs9918104	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv515987	chr5:59128754-59140876	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59110400-59139000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr5:59128200-59160400	Weak transcription	Aorta	Aorta
3	chr5:59129800-59143000	Weak transcription	Fetal Brain Male	brain
4	chr5:59134600-59141400	Weak transcription	Primary B cells from cord blood	blood
5	chr5:59135200-59139600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:59136600-59139000	Weak transcription	HSMMtube	muscle
7	chr5:59136600-59139400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:59136800-59139000	Weak transcription	HSMM	muscle
9	chr5:59137200-59139000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:59137200-59139000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:59137200-59143400	Enhancers	Hela-S3	cervix
12	chr5:59137800-59139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:59137800-59139200	Weak transcription	NH-A	brain
14	chr5:59138000-59139000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:59138000-59139200	Weak transcription	NHLF	lung
16	chr5:59138000-59141000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:59138200-59140600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:59138600-59139600	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links