Variant report

Variant	rs6472412
Chromosome Location	chr8:50294643-50294644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11785374	0.87[ASN][1000 genomes]
rs13277322	0.87[ASN][1000 genomes]
rs1401822	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1519826	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1533667	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533668	0.83[ASN][1000 genomes]
rs1674234	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1674235	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1674258	0.81[AFR][1000 genomes]
rs2385349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828647	0.87[ASN][1000 genomes]
rs7839023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643595	0.85[ASN][1000 genomes]
rs9792112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025068	chr8:49953397-50370208	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1034908	chr8:50023423-50416049	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv539601	chr8:50023423-50416049	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1024410	chr8:50037085-50511501	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv890857	chr8:50133485-50469764	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv917031	chr8:50207246-50709286	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv890858	chr8:50219675-50532935	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv890859	chr8:50253358-50359113	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS 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
rs6472412	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50292400-50295000	Enhancers	Fetal Lung	lung
2	chr8:50293600-50295000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr8:50294000-50295000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr8:50294000-50295000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:50294000-50295000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr8:50294200-50294800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr8:50294200-50294800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr8:50294200-50294800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr8:50294200-50294800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:50294200-50295000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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

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