Variant report

Variant	rs3959554
Chromosome Location	chr15:41443924-41443925
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	chr15:41246285..41249208-chr15:41442914..41444536,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128965	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11852799	1.00[ASN][1000 genomes]
rs11857484	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2013359	0.84[ASN][1000 genomes]
rs28547298	0.98[ASN][1000 genomes]
rs28656781	1.00[ASN][1000 genomes]
rs28770904	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28809504	0.95[ASN][1000 genomes]
rs28874085	0.97[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28880687	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2928155	1.00[ASN][1000 genomes]
rs2955810	0.95[ASN][1000 genomes]
rs35722320	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3986303	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs561821	0.98[ASN][1000 genomes]
rs58330134	0.95[ASN][1000 genomes]
rs61648937	0.87[ASN][1000 genomes]
rs72737713	0.82[ASN][1000 genomes]
rs72737734	0.95[ASN][1000 genomes]
rs73396323	0.95[ASN][1000 genomes]
rs8023991	1.00[ASN][1000 genomes]
rs8030657	1.00[ASN][1000 genomes]
rs8030965	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8031159	0.98[ASN][1000 genomes]
rs9888708	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv904109	chr15:41410705-41481254	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv10980	chr15:41423683-41445889	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3959554	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs3959554	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs3959554	NDUFAF1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41443000-41445600	Weak transcription	HepG2	liver
2	chr15:41443800-41444000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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