Variant report

Variant	rs9289581
Chromosome Location	chr3:139405842-139405843
allele	G/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	EBF1	chr3:139405725-139406046	GM12878	blood:	n/a	chr3:139405882-139405893 chr3:139405884-139405893 chr3:139405882-139405895
2	BATF	chr3:139405748-139406001	GM12878	blood:	n/a	chr3:139405851-139405861 chr3:139405850-139405861
3	EBF1	chr3:139405683-139406104	GM12878	blood:	n/a	chr3:139405882-139405893 chr3:139405884-139405893 chr3:139405882-139405895
4	EBF1	chr3:139405670-139406009	GM12878	blood:	n/a	chr3:139405882-139405893 chr3:139405884-139405893 chr3:139405882-139405895
5	BATF	chr3:139405734-139405943	GM12878	blood:	n/a	chr3:139405851-139405861 chr3:139405850-139405861

No.	Distal block	Cell Line	Cell type
1	chr3:139404964..139406658-chr3:139409631..139411232,2	K562	blood:
2	chr3:139404630..139407387-chr3:139410965..139413960,2	MCF-7	breast:
3	chr3:139404409..139407815-chr3:139408609..139412538,3	K562	blood:

Variant related genes	Relation type
ENSG00000261763	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10935341	0.96[ASN][1000 genomes]
rs12186041	1.00[ASN][1000 genomes]
rs12632145	0.90[ASN][1000 genomes]
rs12634170	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16849303	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs16849305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16849307	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs16849309	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs35449667	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657101	1.00[ASN][1000 genomes]
rs3922940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4474999	0.84[ASN][1000 genomes]
rs4518082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535184	1.00[ASN][1000 genomes]
rs4549242	0.97[ASN][1000 genomes]
rs4615039	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56711752	0.99[ASN][1000 genomes]
rs57304307	1.00[ASN][1000 genomes]
rs59476496	0.94[ASN][1000 genomes]
rs62270189	0.90[ASN][1000 genomes]
rs62270193	0.90[ASN][1000 genomes]
rs62273120	0.97[ASN][1000 genomes]
rs62273121	0.97[ASN][1000 genomes]
rs62273122	0.94[ASN][1000 genomes]
rs6808215	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71627866	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7617537	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636269	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7651551	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9810049	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs9815708	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs9833539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9836944	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9848375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865942	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871543	1.00[ASN][1000 genomes]
rs9874829	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs9878498	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9289581	NMNAT3	cis	multi-tissue	Pritchard
rs9289581	NMNAT3	cis	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139397000-139406800	Weak transcription	Psoas Muscle	Psoas
2	chr3:139397400-139406000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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