Variant report

Variant	rs13201929
Chromosome Location	chr6:117605991-117605992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11966946	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13197910	0.81[JPT][hapmap];0.87[AFR][1000 genomes]
rs13199476	0.86[AFR][1000 genomes]
rs1894674	1.00[LWK][hapmap]
rs2301485	1.00[LWK][hapmap]
rs34228274	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34262053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35829151	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3798366	0.81[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3822947	0.86[AFR][1000 genomes]
rs483223	0.95[CHD][hapmap];0.81[JPT][hapmap]
rs485768	0.91[CHD][hapmap];0.81[JPT][hapmap]
rs497186	1.00[LWK][hapmap]
rs507280	1.00[LWK][hapmap];0.87[AFR][1000 genomes]
rs526306	0.81[JPT][hapmap];0.87[AFR][1000 genomes]
rs528633	1.00[LWK][hapmap]
rs529038	0.91[CHD][hapmap];0.81[JPT][hapmap]
rs529156	0.91[CHD][hapmap];0.81[JPT][hapmap]
rs554017	0.87[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948766	chr6:117407275-117641016	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2758076	chr6:117431224-117627275	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2759465	chr6:117431224-117627275	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830785	chr6:117448943-117627275	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2757190	chr6:117464048-117609529	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Myopia (pathological)	23049088	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13201929	RFX6	cis	cerebellum	SCAN
rs13201929	FAM26E	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117605200-117606000	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr6:117605400-117606000	Enhancers	Skeletal Muscle Male	skeletal muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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