Variant report

Variant	rs4389440
Chromosome Location	chr3:139437613-139437614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139437070..139437910-chr3:139653098..139654016,8	MCF-7	breast:
2	chr3:139437002..139437900-chr3:139652880..139654338,15	MCF-7	breast:
3	chr3:139436698..139437886-chr3:139769877..139770897,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158258	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10804670	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10804671	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935342	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs10935345	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935346	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935347	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710180	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712200	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713380	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714937	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717128	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717212	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718071	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718895	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718996	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720033	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720876	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11921973	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629519	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073922	0.99[ASN][1000 genomes]
rs35021375	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074740	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4075288	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4234476	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234477	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306820	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4327348	0.98[ASN][1000 genomes]
rs4428139	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4504138	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4528899	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530491	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532090	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4549243	0.99[ASN][1000 genomes]
rs4640519	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4683679	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683681	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683684	1.00[ASN][1000 genomes]
rs55638024	0.81[ASN][1000 genomes]
rs56788591	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58001126	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60644900	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62270187	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62270188	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785099	0.85[ASN][1000 genomes]
rs6798004	0.81[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs73223019	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73866609	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7427023	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7639511	0.90[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7648532	1.00[ASN][1000 genomes]
rs7649565	1.00[ASN][1000 genomes]
rs9683206	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9813439	1.00[ASN][1000 genomes]
rs9822952	0.87[JPT][hapmap]
rs9823295	1.00[ASN][1000 genomes]
rs9838164	0.99[ASN][1000 genomes]
rs9876534	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9876555	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv460865	chr3:139411031-139455326	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv591857	chr3:139411031-139455326	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4389440	NMNAT3	cis	Lymphoblastoid	GTEx
rs4389440	NMNAT3	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139434600-139437800	Enhancers	HSMMtube	muscle
2	chr3:139435400-139437800	Enhancers	Fetal Stomach	stomach
3	chr3:139436400-139437800	Enhancers	Fetal Brain Female	brain
4	chr3:139437200-139437800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:139437200-139437800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:139437200-139437800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:139437200-139437800	Enhancers	Fetal Muscle Trunk	muscle
8	chr3:139437400-139437800	Weak transcription	Ovary	ovary
9	chr3:139437400-139440000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:139437600-139437800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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