Variant report

Variant	rs5006575
Chromosome Location	chr4:87037379-87037380
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10024003	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10212952	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097094	0.93[AFR][1000 genomes]
rs11943376	0.85[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12505566	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12640395	0.85[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4377581	0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4530621	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4693135	0.85[ASW][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4693754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57376960	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6531898	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6821745	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6822478	0.82[CHD][hapmap]
rs7435363	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2754254	chr4:86979147-87108510	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv879521	chr4:86979927-87165758	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1005338	chr4:87023398-87108555	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5006575	NUDT9	cis	parietal	SCAN
rs5006575	PTPN13	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87005000-87050400	Weak transcription	Brain Angular Gyrus	brain
2	chr4:87023400-87038800	Weak transcription	Brain Anterior Caudate	brain
3	chr4:87030400-87038400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:87035800-87077600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:87036200-87038200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:87036400-87041200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:87036600-87038000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:87036600-87038800	Weak transcription	Fetal Stomach	stomach
9	chr4:87036600-87039200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:87037000-87040200	Enhancers	NHDF-Ad	bronchial
11	chr4:87037200-87039000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

Quick Search:

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

what's new

Quick links