Variant report

Variant	rs9939485
Chromosome Location	chr16:71207879-71207880
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1155051	0.87[JPT][hapmap]
rs1155052	0.82[ASN][1000 genomes]
rs1155054	0.82[ASN][1000 genomes]
rs12447448	0.87[JPT][hapmap]
rs12448046	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs13332757	0.84[ASN][1000 genomes]
rs1364279	0.87[JPT][hapmap]
rs1424134	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1424136	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1424137	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1557761	0.84[ASN][1000 genomes]
rs1559420	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1895528	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2042423	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2081253	0.82[ASN][1000 genomes]
rs2098746	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2158102	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2883938	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs3114634	0.96[ASN][1000 genomes]
rs3743954	0.87[JPT][hapmap]
rs3785346	0.82[ASN][1000 genomes]
rs3902443	0.82[ASN][1000 genomes]
rs4636918	0.83[ASN][1000 genomes]
rs4788529	0.83[ASN][1000 genomes]
rs4788534	0.83[ASN][1000 genomes]
rs4788536	0.82[ASN][1000 genomes]
rs7190305	0.87[JPT][hapmap]
rs7193051	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7498840	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs757106	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs764600	0.84[ASN][1000 genomes]
rs8052442	0.81[ASN][1000 genomes]
rs9924525	0.84[ASN][1000 genomes]
rs9928164	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs9930115	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs9932494	0.85[ASN][1000 genomes]
rs9934283	0.87[JPT][hapmap]
rs9934510	0.82[ASN][1000 genomes]
rs9936905	0.83[ASN][1000 genomes]
rs9939194	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9939836	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs9940569	0.87[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059478	chr16:70773597-71237055	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	esv2758429	chr16:70807122-71316983	Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2758653	chr16:70807122-71316983	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1059620	chr16:70848374-71237055	Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542944	chr16:70848374-71237055	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1060754	chr16:71008303-71276778	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9939485	NUTF2	cis	cerebellum	SCAN
rs9939485	DHODH	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71194200-71216200	Weak transcription	Brain Anterior Caudate	brain
2	chr16:71196600-71218800	Weak transcription	Fetal Kidney	kidney
3	chr16:71206600-71209600	Enhancers	Brain Germinal Matrix	brain
4	chr16:71206600-71210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:71206800-71217400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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