Variant report

Variant	rs12004623
Chromosome Location	chr9:96679358-96679359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96678251..96680846-chr9:96690063..96691952,2	MCF-7	breast:
2	chr9:96670566..96673928-chr9:96676412..96679551,4	K562	blood:
3	chr9:96676732..96679654-chr9:96681245..96683320,2	MCF-7	breast:
4	chr9:96673909..96678084-chr9:96678410..96682250,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10123220	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10761305	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10761306	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10821261	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821262	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821264	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992992	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11787549	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11791552	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11791598	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11794101	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12337696	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12344756	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349429	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12350414	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12353447	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13295144	0.80[ASN][1000 genomes]
rs34589520	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34652157	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34880630	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743937	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744301	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744302	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1053137	chr9:96644876-96683214	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1046904	chr9:96647940-96689327	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1035418	chr9:96647940-96711409	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv1801607	chr9:96657324-96683214	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1042043	chr9:96657324-96689327	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3356472	chr9:96677831-96682029	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12004623	NFIL3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96671400-96679600	Weak transcription	Gastric	stomach
2	chr9:96677000-96685200	Weak transcription	Spleen	Spleen
3	chr9:96679000-96680000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:96679000-96682600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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