Variant report

Variant	rs2978548
Chromosome Location	chr8:62145104-62145105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10090442	0.82[ASN][1000 genomes]
rs13278769	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1367974	1.00[JPT][hapmap]
rs1968908	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2052993	1.00[JPT][hapmap]
rs2119228	0.82[ASN][1000 genomes]
rs2919303	0.82[JPT][hapmap]
rs2919305	0.81[ASW][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs2919311	0.82[ASN][1000 genomes]
rs2919312	0.82[ASN][1000 genomes]
rs2919313	0.82[ASN][1000 genomes]
rs2919314	0.82[ASN][1000 genomes]
rs2919315	0.82[ASN][1000 genomes]
rs2931284	1.00[ASN][1000 genomes]
rs2931285	0.82[ASN][1000 genomes]
rs2931286	0.82[ASN][1000 genomes]
rs2931292	0.82[JPT][hapmap]
rs2931295	0.82[ASN][1000 genomes]
rs2931322	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2931323	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2931346	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2931351	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2931353	0.95[ASN][1000 genomes]
rs2931354	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2931355	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2931356	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2978491	0.82[ASN][1000 genomes]
rs2978498	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2978542	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2978547	0.92[EUR][1000 genomes]
rs2978550	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2978552	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2978558	0.82[JPT][hapmap]
rs34574871	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4100940	0.82[ASN][1000 genomes]
rs6983455	1.00[JPT][hapmap]
rs7017483	1.00[JPT][hapmap]
rs7017626	1.00[JPT][hapmap]
rs7818621	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7834568	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838220	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7838580	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964784	0.86[ASN][1000 genomes]
rs9650205	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv948922	chr8:61818964-62475097	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv465698	chr8:62036793-62179465	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv611426	chr8:62036793-62179465	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1024432	chr8:62086247-62898782	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2978548	CLVS1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:62137200-62146200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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