Variant report

Variant	rs16902409
Chromosome Location	chr5:35684832-35684833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10064741	0.85[EUR][1000 genomes]
rs10067949	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10069995	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10079528	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[EUR][1000 genomes]
rs11748763	1.00[ASW][hapmap];0.84[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13177154	0.84[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16902418	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34682820	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6451205	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72738827	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7710864	0.89[YRI][hapmap]
rs7721708	0.89[YRI][hapmap]
rs9292604	0.83[CEU][hapmap]
rs9292607	0.87[EUR][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	nsv525477	chr5:35530905-35792990	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv880510	chr5:35659239-35709184	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv881146	chr5:35659239-35714851	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1843371	chr5:35668036-35706279	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16902409	NIPBL	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35630600-35707600	Weak transcription	Pancreas	Pancrea
2	chr5:35672000-35708600	Weak transcription	Gastric	stomach
3	chr5:35673600-35693400	Weak transcription	Brain Anterior Caudate	brain
4	chr5:35673600-35694600	Weak transcription	Brain Angular Gyrus	brain
5	chr5:35679800-35685200	Weak transcription	Left Ventricle	heart
6	chr5:35680000-35698600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr5:35681000-35707600	Weak transcription	Primary T cells from cord blood	blood
8	chr5:35684400-35686200	Enhancers	Fetal Heart	heart
9	chr5:35684600-35685000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:35684600-35685600	Weak transcription	Fetal Lung	lung
11	chr5:35684600-35708600	Weak transcription	Fetal Kidney	kidney
12	chr5:35684800-35703600	Weak transcription	Fetal Intestine Small	intestine

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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