Variant report

Variant	rs273653
Chromosome Location	chr19:51740839-51740840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1399839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166653	0.84[CEU][hapmap]
rs1697531	0.92[CEU][hapmap]
rs1710381	0.88[CEU][hapmap]
rs2249782	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs273619	0.84[CEU][hapmap]
rs273642	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs273644	0.88[CEU][hapmap]
rs273646	0.88[CEU][hapmap]
rs273647	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs273648	0.91[CEU][hapmap]
rs273649	0.92[CEU][hapmap]
rs273650	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs273651	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs273652	0.92[CEU][hapmap]
rs62115996	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs273653	NLRP9	cis	parietal	SCAN
rs273653	ZNF134	cis	parietal	SCAN
rs273653	ZNF444	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51731000-51748800	Weak transcription	K562	blood
2	chr19:51733400-51744200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr19:51734200-51744200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr19:51735200-51743000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr19:51735800-51743600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:51736200-51743000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:51736400-51743000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:51736400-51744000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:51736800-51744000	Weak transcription	Spleen	Spleen
10	chr19:51739000-51748800	Weak transcription	Adipose Nuclei	Adipose
11	chr19:51739800-51742400	Strong transcription	Primary hematopoietic stem cells	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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