Variant report

Variant	rs1030462
Chromosome Location	chr5:116748877-116748878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr5:116748869-116749153	HepG2	liver:	n/a	chr5:116748986-116749002 chr5:116748986-116749001
2	GATA3	chr5:116748535-116748905	MCF-7	breast:	n/a	chr5:116748757-116748770
3	GATA3	chr5:116748482-116748952	MCF-7	breast:	n/a	chr5:116748757-116748770

Variant related genes	Relation type
LINC00992	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10065401	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10075994	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11241424	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13164082	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13183369	0.87[ASN][1000 genomes]
rs13358449	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13358452	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1428048	0.94[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2007303	0.83[ASN][1000 genomes]
rs2560593	0.83[ASN][1000 genomes]
rs2560595	0.81[ASN][1000 genomes]
rs2624459	0.83[ASN][1000 genomes]
rs2624462	0.82[ASN][1000 genomes]
rs2900102	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4455596	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4481381	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4587112	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4920870	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4920871	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4920965	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6875942	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7714703	0.91[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7732741	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs950073	0.83[ASN][1000 genomes]
rs950074	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882755	chr5:116647725-116748877	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830457	chr5:116724777-116875060	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv599487	chr5:116732456-116772093	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1030462	COMMD10	cis	parietal	SCAN
rs1030462	SEMA6A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116748800-116752600	Weak transcription	Fetal Lung	lung

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