Variant report

Variant	rs6534090
Chromosome Location	chr4:79865281-79865282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79859950..79862790-chr4:79863259..79866666,3	K562	blood:

Variant related genes	Relation type
ENSG00000163291	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10018189	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10025599	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10034295	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10857059	0.85[MEX][hapmap]
rs11722437	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1275045	0.84[AMR][1000 genomes]
rs1275046	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1275047	0.80[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1299129	0.85[MEX][hapmap]
rs13108247	0.80[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1383425	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1383426	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1480718	0.85[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1480733	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1825022	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1871706	0.85[MEX][hapmap]
rs1979444	0.80[CHB][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2046104	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288254	0.85[CHB][hapmap]
rs3822106	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs3937772	0.84[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4512020	0.80[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4576033	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62308043	0.92[ASN][1000 genomes]
rs6534083	0.80[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6534085	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6534086	0.84[ASN][1000 genomes]
rs6534087	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6846743	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6854347	0.80[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs725500	0.93[ASN][1000 genomes]
rs7656083	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7664339	0.93[CEU][hapmap];0.85[MEX][hapmap]
rs7664587	0.85[MEX][hapmap]
rs7677084	0.87[CEU][hapmap];0.90[MEX][hapmap]
rs7688534	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs931149	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs931150	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9993426	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879504	chr4:79759796-79874275	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6534090	NAAA	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79863200-79865400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr4:79863200-79865600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr4:79865200-79866200	Enhancers	Fetal Intestine Small	intestine

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