Variant report

Variant	rs12742405
Chromosome Location	chr1:76907906-76907907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11581788	0.85[ASN][1000 genomes]
rs11806270	1.00[YRI][hapmap]
rs12068326	1.00[ASW][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12756608	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12757663	0.83[MKK][hapmap];0.82[YRI][hapmap]
rs12759169	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35789244	0.95[AMR][1000 genomes]
rs36017719	1.00[AFR][1000 genomes]
rs7529530	1.00[ASW][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]

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	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv462006	chr1:76826279-77042405	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv546585	chr1:76826279-77042405	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv947115	chr1:76906026-76910246	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12742405	ST6GALNAC3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76905600-76910800	Weak transcription	Fetal Heart	heart
2	chr1:76907600-76908200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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