Variant report

Variant	rs273619
Chromosome Location	chr19:51759936-51759937
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	MAFK	chr19:51759857-51760043	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SIGLECL1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11084065	0.82[CHD][hapmap]
rs1399839	0.84[CEU][hapmap]
rs166653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs169275	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1697531	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1697566	0.82[CHD][hapmap];0.89[GIH][hapmap]
rs1710381	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2249782	0.92[CEU][hapmap]
rs273641	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs273643	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs273644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs273646	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs273647	0.92[CEU][hapmap]
rs273648	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs273649	0.96[CEU][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs273650	0.88[CEU][hapmap]
rs273651	0.88[CEU][hapmap]
rs273652	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs273653	0.84[CEU][hapmap]
rs9676731	0.82[JPT][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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv518134	chr19:51750238-51765953	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv1060026	chr19:51751123-51773175	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs273619	NLRP9	cis	parietal	SCAN
rs273619	ZNF134	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51757400-51761000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr19:51757600-51761200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr19:51759400-51761400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:51759400-51761400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:51759400-51762800	Enhancers	Primary hematopoietic stem cells	blood
6	chr19:51759400-51762800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr19:51759600-51761600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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