Variant report

Variant	rs2112496
Chromosome Location	chr5:119564492-119564493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1015728	0.80[ASN][1000 genomes]
rs1023614	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11241537	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11241538	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11740198	0.89[EUR][1000 genomes]
rs11748728	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11954557	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11954582	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12515922	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12522109	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12719272	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13171622	0.89[EUR][1000 genomes]
rs13185135	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13360069	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1422378	0.85[EUR][1000 genomes]
rs1422381	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422382	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422383	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422384	0.84[EUR][1000 genomes]
rs1582471	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1592902	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1862293	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2032825	0.89[EUR][1000 genomes]
rs2032826	0.88[EUR][1000 genomes]
rs2161264	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2161265	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2161266	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34067116	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6595219	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6595220	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67145013	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6863983	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879144	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879167	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6883360	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6887881	0.91[EUR][1000 genomes]
rs7711749	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7732018	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7732463	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023146	chr5:119301891-119623417	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537883	chr5:119301891-119623417	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv432803	chr5:119419101-119659101	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv882782	chr5:119526332-119627087	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv882783	chr5:119532996-119605609	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
7	nsv882784	chr5:119537259-119606988	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv882785	chr5:119557828-119606988	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv3329556	chr5:119558102-119587922	Enhancers Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2112496	IKZF1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119561400-119570600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:119564200-119564600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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