Variant report

Variant	rs1500138
Chromosome Location	chr5:79613941-79613942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10040789	0.86[ASN][1000 genomes]
rs10040794	0.86[ASN][1000 genomes]
rs10056190	0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10059140	0.88[CEU][hapmap]
rs10062770	1.00[JPT][hapmap]
rs10942920	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12654082	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12655069	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1862136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2112151	0.86[ASN][1000 genomes]
rs2161093	0.86[ASN][1000 genomes]
rs2216548	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4286649	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4478300	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4703808	0.93[ASN][1000 genomes]
rs4703809	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704661	0.82[ASN][1000 genomes]
rs6453514	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453515	0.87[ASN][1000 genomes]
rs6859753	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6866850	0.83[YRI][hapmap]
rs6897248	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7718110	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap]
rs7720696	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7722090	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap]
rs7734893	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7735071	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv518480	chr5:79586085-79748382	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv980690	chr5:79591958-79614381	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1500138	TMEM167A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79613600-79614600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr5:79613800-79614200	Enhancers	Brain Anterior Caudate	brain
3	chr5:79613800-79614400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:79613800-79614600	Enhancers	NHDF-Ad	bronchial
5	chr5:79613800-79614800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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