Variant report

Variant	rs17104490
Chromosome Location	chr14:68080560-68080561
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	MYC	chr14:68080077-68080619	A549	lung:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARG2-2	chr14:68080267-68080581	NONHSAT037455

Variant related genes	Relation type
ENSG00000259648	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10459532	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs1059238	0.83[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1120877	0.83[CEU][hapmap]
rs11622441	0.86[EUR][1000 genomes]
rs11623700	0.82[ASW][hapmap];0.83[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11623785	0.83[CEU][hapmap]
rs11623961	0.83[CEU][hapmap]
rs11624498	0.86[EUR][1000 genomes]
rs11624868	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11625839	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11628860	0.86[EUR][1000 genomes]
rs12050393	0.82[ASW][hapmap];0.83[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1555193	0.83[CEU][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap]
rs17104526	0.84[EUR][1000 genomes]
rs17104544	0.83[CEU][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs17104550	0.85[EUR][1000 genomes]
rs17249472	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs2234511	0.86[EUR][1000 genomes]
rs2320029	0.95[GIH][hapmap]
rs28390085	0.83[EUR][1000 genomes]
rs28532066	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3742880	0.82[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs3742881	0.82[ASW][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4899222	0.82[ASW][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap]
rs4902506	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs4902508	0.88[EUR][1000 genomes]
rs56083029	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56244142	0.88[EUR][1000 genomes]
rs56256221	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6573790	0.91[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs7140310	0.83[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs7142897	0.88[EUR][1000 genomes]
rs7144186	0.81[CEU][hapmap];0.85[AMR][1000 genomes]
rs7144243	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7148327	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs7151205	0.86[EUR][1000 genomes]
rs7151230	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152326	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs7155788	0.83[EUR][1000 genomes]
rs72721082	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72721090	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72723111	0.86[EUR][1000 genomes]
rs72723115	0.86[EUR][1000 genomes]
rs72723122	0.88[EUR][1000 genomes]
rs72723126	0.88[EUR][1000 genomes]
rs72723137	0.88[EUR][1000 genomes]
rs72723144	0.88[EUR][1000 genomes]
rs761513	0.82[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs761514	0.86[EUR][1000 genomes]
rs8009250	0.85[EUR][1000 genomes]
rs8013767	0.82[ASW][hapmap];0.83[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs8020591	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17104490	ZBTB1	cis	cerebellum	SCAN
rs17104490	RDH11	Cis_1M	lymphoblastoid	RTeQTL
rs17104490	C14orf162	cis	parietal	SCAN
rs17104490	RDH11	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68076800-68086200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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