Variant report

Variant	rs1126478
Chromosome Location	chr3:46501213-46501214
allele	A/G
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	chr3:46500816-46501246	HL-60	blood:	n/a	chr3:46501053-46501060

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46501096..46502745-chr3:46502800..46504664,2	K562	blood:
2	chr3:46499839..46502077-chr3:46515720..46518356,2	K562	blood:

Variant related genes	Relation type
LTF	TF binding region

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1042073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130091	0.80[CEU][hapmap]
rs11707471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716497	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1475967	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2269435	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2269437	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2269438	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2269439	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2269440	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2269442	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4234463	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4682816	0.89[ASN][1000 genomes]
rs4683228	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4683234	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6441990	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs6441992	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap]
rs6441995	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6776504	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6778559	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6787643	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6794622	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs743659	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap]
rs7624071	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862186	0.81[CEU][hapmap]
rs9862388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

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	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1126478	PTPN23	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46480200-46504000	Weak transcription	Lung	lung
2	chr3:46489400-46504000	Weak transcription	Right Atrium	heart
3	chr3:46497800-46503600	Weak transcription	Gastric	stomach
4	chr3:46497800-46504000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:46498000-46504800	Weak transcription	Pancreas	Pancrea
6	chr3:46500000-46503800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr3:46501000-46501400	Enhancers	Left Ventricle	heart
8	chr3:46501000-46502200	Genic enhancers	Spleen	Spleen
9	chr3:46501200-46501400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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