Variant report

Variant	rs34748201
Chromosome Location	chr15:77221530-77221531
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	POLR2A	chr15:77221516-77221618	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:77195473..77197812-chr15:77219400..77222194,2	K562	blood:
2	chr15:77194744..77199863-chr15:77220881..77225601,7	MCF-7	breast:
3	chr15:77213948..77217003-chr15:77220696..77223782,5	K562	blood:
4	chr15:77209000..77210645-chr15:77221529..77223671,2	K562	blood:

Variant related genes	Relation type
RCN2	TF binding region
ENSG00000140386	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12148386	0.90[ASN][1000 genomes]
rs12438362	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441855	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12595586	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12909665	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913810	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12916324	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17380507	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17464903	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34338978	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35076986	0.95[ASN][1000 genomes]
rs35157989	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35999717	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3829489	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360890	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886507	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886839	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56234001	0.97[ASN][1000 genomes]
rs58889902	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66508953	0.91[ASN][1000 genomes]
rs71398948	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166156	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169663	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8024737	0.91[ASN][1000 genomes]
rs9788684	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][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	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking 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 miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34748201	SCAPER	cis	Nerve Tibial	GTEx
rs34748201	SCAPER	cis	Artery Tibial	GTEx
rs34748201	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs34748201	SCAPER	cis	lung	GTEx
rs34748201	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77220600-77221800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:77220600-77222200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr15:77220800-77223000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:77221200-77223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:77221200-77223400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:77221400-77221600	Enhancers	Brain Anterior Caudate	brain
7	chr15:77221400-77222200	Enhancers	HUES64 Cell Line	embryonic stem cell

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