Variant report

Variant	rs12530017
Chromosome Location	chr6:38853427-38853428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12524328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12524938	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]
rs12526772	0.83[CEU][hapmap]
rs12526788	0.83[CEU][hapmap]
rs12528676	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]
rs1564376	0.83[CEU][hapmap]
rs17624428	0.83[CEU][hapmap];0.90[MEX][hapmap]
rs17632805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2038199	0.83[CEU][hapmap]
rs2038200	0.83[CEU][hapmap]
rs2038201	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap]
rs2038202	0.83[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap]
rs2038203	0.83[CEU][hapmap]
rs2050179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2179710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7749015	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap]
rs7773138	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap]

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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12530017	GLO1	cis	cerebellum	SCAN
rs12530017	SLC26A8	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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