Variant report

Variant	rs6453906
Chromosome Location	chr6:77176775-77176776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1038751	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1155343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11965526	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12201715	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1490208	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1490211	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1602255	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2314709	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2872724	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4305690	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4598032	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4598033	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6453902	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6453903	0.98[EUR][1000 genomes]
rs6453904	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6453905	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6907639	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6916882	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6916992	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6917291	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6941851	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7739183	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7754323	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7756845	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7757654	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7757747	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7759390	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs884044	0.96[EUR][1000 genomes]
rs9443242	0.87[CHB][hapmap]
rs9447700	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1025439	chr6:77093795-77479689	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538320	chr6:77093795-77479689	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv886204	chr6:77103194-77208816	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv886205	chr6:77103194-77266188	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv830699	chr6:77111857-77291223	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv886206	chr6:77130167-77208816	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv886207	chr6:77130167-77266188	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv886208	chr6:77130167-77317683	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv886209	chr6:77138302-77208816	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6453906	SLC39A8	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:77176000-77176800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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