Variant report

Variant	rs12651516
Chromosome Location	chr4:77001005-77001006
allele	C/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	RCOR1	chr4:77000993-77001017	K562	blood:	n/a	n/a
2	E2F4	chr4:77000999-77001116	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76999683..77002474-chr4:77050888..77053067,2	K562	blood:

Variant related genes	Relation type
ART3	TF binding region
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10518144	0.83[ASN][1000 genomes]
rs10654	0.83[ASN][1000 genomes]
rs1127695	0.83[ASN][1000 genomes]
rs11725358	0.80[ASN][1000 genomes]
rs11726372	0.82[ASN][1000 genomes]
rs11729637	0.80[ASN][1000 genomes]
rs11733489	0.80[ASN][1000 genomes]
rs17001364	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17001390	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17001422	0.81[ASN][1000 genomes]
rs17001424	0.83[ASN][1000 genomes]
rs17001433	0.83[ASN][1000 genomes]
rs33997696	0.83[ASN][1000 genomes]
rs34747816	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41349449	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41411447	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41498548	0.82[ASN][1000 genomes]
rs4256246	0.84[AFR][1000 genomes]
rs4308383	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4403073	0.83[ASN][1000 genomes]
rs4408983	0.83[ASN][1000 genomes]
rs4859418	0.81[EUR][1000 genomes]
rs4859420	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56669417	0.82[ASN][1000 genomes]
rs56670659	0.84[ASN][1000 genomes]
rs56788469	0.82[ASN][1000 genomes]
rs56887664	0.81[ASN][1000 genomes]
rs57268096	0.84[ASN][1000 genomes]
rs57960366	0.82[ASN][1000 genomes]
rs58127619	0.81[ASN][1000 genomes]
rs58232272	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58319866	0.82[ASN][1000 genomes]
rs58358710	0.80[ASN][1000 genomes]
rs58380268	0.83[ASN][1000 genomes]
rs58510808	0.83[ASN][1000 genomes]
rs59547714	0.84[ASN][1000 genomes]
rs59765882	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59789355	0.83[ASN][1000 genomes]
rs60160936	0.82[ASN][1000 genomes]
rs60387070	0.83[ASN][1000 genomes]
rs60573877	0.81[ASN][1000 genomes]
rs60610578	0.83[ASN][1000 genomes]
rs61099048	0.80[ASN][1000 genomes]
rs61293119	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61369069	0.82[ASN][1000 genomes]
rs61693363	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62299341	0.82[ASN][1000 genomes]
rs62299342	0.81[ASN][1000 genomes]
rs62299348	0.82[ASN][1000 genomes]
rs62299349	0.82[ASN][1000 genomes]
rs62299350	0.82[ASN][1000 genomes]
rs62299354	0.82[ASN][1000 genomes]
rs62299355	0.82[ASN][1000 genomes]
rs62318915	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62318924	0.83[ASN][1000 genomes]
rs62318925	0.83[ASN][1000 genomes]
rs62318926	0.83[ASN][1000 genomes]
rs62318928	0.83[ASN][1000 genomes]
rs62318929	0.83[ASN][1000 genomes]
rs6532201	0.82[ASN][1000 genomes]
rs6836715	0.86[ASN][1000 genomes]
rs6838303	0.86[ASN][1000 genomes]
rs6840007	0.82[ASN][1000 genomes]
rs7656282	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7656734	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657846	0.82[ASN][1000 genomes]
rs7661431	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7662240	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7664821	0.83[ASN][1000 genomes]
rs7666848	0.82[ASN][1000 genomes]
rs7668507	0.80[ASN][1000 genomes]
rs7670483	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7675107	0.83[ASN][1000 genomes]
rs7675618	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7679084	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7679283	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7679611	0.83[ASN][1000 genomes]
rs7690763	0.81[ASN][1000 genomes]
rs7695601	0.83[ASN][1000 genomes]
rs7697701	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12651516	NUP54	cis	Nerve Tibial	GTEx
rs12651516	NUP54	cis	Thyroid	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76997000-77007200	Weak transcription	Fetal Brain Male	brain
2	chr4:76997000-77008000	Weak transcription	Brain Angular Gyrus	brain
3	chr4:76999000-77008200	Weak transcription	Right Ventricle	heart
4	chr4:76999400-77004200	Weak transcription	Psoas Muscle	Psoas
5	chr4:76999600-77008000	Weak transcription	Liver	Liver
6	chr4:77001000-77001600	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr4:77001000-77003400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr4:77001000-77005800	Weak transcription	Fetal Heart	heart
9	chr4:77001000-77006200	Weak transcription	Left Ventricle	heart

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