Variant report

Variant	rs11717932
Chromosome Location	chr3:34240347-34240348
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	SPI1	chr3:34239768-34240367	GM12878	blood:	n/a	n/a
2	FOXA1	chr3:34240112-34240416	T-47D	breast:	n/a	chr3:34240246-34240258
3	FOXA2	chr3:34240091-34240426	A549	lung:	n/a	chr3:34240246-34240258
4	EBF1	chr3:34239821-34240522	GM12878	blood:	n/a	chr3:34240351-34240362 chr3:34240351-34240364
5	FOXA1	chr3:34240013-34240379	T-47D	breast:	n/a	chr3:34240246-34240258
6	FOXA2	chr3:34240004-34240422	A549	lung:	n/a	chr3:34240246-34240258

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:34238738..34241610-chr3:34244230..34246747,2	K562	blood:

Variant related genes	Relation type
ENSG00000236452	TF binding region
ENSG00000236452	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10510658	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129588	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129589	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11129590	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708781	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710773	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714874	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920101	0.81[EUR][1000 genomes]
rs11927616	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927965	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063086	1.00[CHB][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065915	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079510	0.83[EUR][1000 genomes]
rs13083357	1.00[CHB][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866754	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960959	1.00[ASN][1000 genomes]
rs62248462	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66558495	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789334	1.00[ASN][1000 genomes]
rs7612155	1.00[ASN][1000 genomes]
rs7621412	1.00[CHB][hapmap]
rs7626572	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627333	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968102	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968103	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	nsv522881	chr3:33736126-34241686	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1001599	chr3:34149575-34437701	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536533	chr3:34149575-34437701	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv876682	chr3:34149814-34401451	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv916961	chr3:34203879-34506554	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11717932	AC123023.1	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:34238000-34242400	Enhancers	Primary B cells from peripheral blood	blood
2	chr3:34238800-34240600	Enhancers	Dnd41	blood
3	chr3:34239000-34242400	Enhancers	Primary B cells from cord blood	blood
4	chr3:34239600-34240800	Enhancers	Fetal Thymus	thymus
5	chr3:34240200-34240400	Enhancers	GM12878-XiMat	blood
6	chr3:34240200-34242400	Weak transcription	Thymus	Thymus

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