Variant report

Variant	rs9998233
Chromosome Location	chr4:76996381-76996382
allele	C/G
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	POLR2A	chr4:76996142-76996780	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
ART3	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10019066	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025961	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030471	1.00[AFR][1000 genomes];1.00[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	0.98[AFR][1000 genomes];1.00[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]
rs12498973	0.92[YRI][hapmap]
rs12499668	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504915	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12509988	1.00[CEU][hapmap]
rs12509996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12510239	1.00[AFR][1000 genomes];1.00[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];1.00[YRI][hapmap]
rs12511357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[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];0.97[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];0.88[MEX][hapmap]
rs13106039	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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];0.88[MEX][hapmap]
rs28484974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647509	1.00[AFR][1000 genomes];1.00[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	0.85[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];0.88[MEX][hapmap]
rs4404571	0.90[ASN][1000 genomes]
rs4621456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56054611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60282049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60431104	1.00[AFR][1000 genomes];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532169	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]
rs6532170	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67194908	1.00[AFR][1000 genomes];1.00[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[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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	0.90[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	0.87[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693117	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693456	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7693606	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7693693	0.84[AFR][1000 genomes];0.97[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];0.88[MEX][hapmap]
rs9990658	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995300	0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][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
rs9998233	NAAA	cis	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76994000-76996600	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr4:76994400-76996400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:76995200-76996400	Enhancers	Brain Anterior Caudate	brain
4	chr4:76995200-76996400	Enhancers	Rectal Smooth Muscle	rectum
5	chr4:76995200-76996600	Enhancers	Colon Smooth Muscle	Colon
6	chr4:76995200-76996600	Enhancers	Stomach Smooth Muscle	stomach
7	chr4:76995400-76996400	Enhancers	HSMMtube	muscle
8	chr4:76995400-76996600	Enhancers	Brain Hippocampus Middle	brain
9	chr4:76995400-76996600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr4:76995400-76997000	Enhancers	Brain Angular Gyrus	brain
11	chr4:76995600-76996800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:76995600-76997000	Enhancers	Brain Substantia Nigra	brain
13	chr4:76995600-76999400	Active TSS	Psoas Muscle	Psoas
14	chr4:76995600-77000800	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr4:76995800-76996400	Weak transcription	Fetal Brain Male	brain
16	chr4:76995800-76996600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:76995800-76996800	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr4:76995800-76997000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr4:76995800-76997000	Enhancers	Fetal Heart	heart
20	chr4:76995800-76997000	Active TSS	Left Ventricle	heart
21	chr4:76995800-76998200	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr4:76995800-76999000	Active TSS	Right Ventricle	heart
23	chr4:76996000-76996600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:76996000-76996800	Active TSS	Right Atrium	heart

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