Variant report

Variant	rs6532169
Chromosome Location	chr4:76995035-76995036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76994585..76995085-chr8:22431839..22432590,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10019066	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025961	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030471	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10222911	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs10433952	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10856871	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs12499668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504339	0.83[YRI][hapmap]
rs12504915	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12509988	1.00[CEU][hapmap]
rs12509996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs12510239	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511352	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12511357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511861	0.83[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs13106039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554015	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs17001275	0.83[CEU][hapmap]
rs17001284	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs28484974	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601861	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647509	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869461	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs35353995	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733236	0.82[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs4404571	0.90[ASN][1000 genomes]
rs4621456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813915	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56054611	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60282049	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60431104	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67194908	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67308118	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67687266	0.84[ASN][1000 genomes]
rs6834291	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs6857378	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666094	1.00[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670156	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7671170	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7671209	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7676234	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7679689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs7684879	0.82[ASN][1000 genomes]
rs7685390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693117	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693456	1.00[CEU][hapmap]
rs7693606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs7693693	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7696286	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs9990658	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6532169	NAAA	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76993400-76996000	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr4:76993400-76996000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr4:76993600-76995800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr4:76993800-76995200	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr4:76993800-76995400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr4:76994000-76995800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:76994000-76996600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:76994400-76995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:76994400-76995600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr4:76994400-76996400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:76994600-76995600	Weak transcription	Psoas Muscle	Psoas
12	chr4:76994800-76995200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:76994800-76995600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:76995000-76995800	Flanking Active TSS	Fetal Heart	heart

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