Variant report

Variant	rs12901241
Chromosome Location	chr15:79002662-79002663
allele	A/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	CTCF	chr15:79001284-79002708	SK-N-SH	brain:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78910051..78911529-chr15:79000733..79002666,9	K562	blood:
2	chr15:78909956..78912504-chr15:79001139..79003801,2	MCF-7	breast:

Variant related genes	Relation type
CHRNB4	TF binding region
ENSG00000080644	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12324870	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12901331	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12905273	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12905641	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28444683	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34067845	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34099810	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34275594	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34422348	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34550457	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34694149	0.85[EUR][1000 genomes]
rs35701817	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35704045	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58526289	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58946838	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61630816	0.85[EUR][1000 genomes]
rs62010555	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62010556	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs67775542	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169223	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178007	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8038920	0.82[EUR][1000 genomes]
rs922691	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12901241	CHRNA5	cis	Muscle Skeletal	GTEx
rs12901241	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79002000-79004800	Weak transcription	NH-A	brain
2	chr15:79002200-79005400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:79002200-79007400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:79002400-79003800	Weak transcription	HepG2	liver
5	chr15:79002600-79004000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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