Variant report

Variant	rs17224545
Chromosome Location	chr4:77025810-77025811
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	chr4:77024140..77027603-chr4:77067488..77070849,3	K562	blood:
2	chr4:77022675..77026827-chr4:77067488..77070849,4	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10518144	0.85[EUR][1000 genomes]
rs10654	0.85[EUR][1000 genomes]
rs1127695	0.85[EUR][1000 genomes]
rs11724260	1.00[ASW][hapmap];0.83[TSI][hapmap]
rs11725358	0.80[EUR][1000 genomes]
rs11726372	0.85[EUR][1000 genomes]
rs11729637	0.85[EUR][1000 genomes]
rs11733489	0.85[EUR][1000 genomes]
rs17001364	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs17001390	0.88[EUR][1000 genomes]
rs17001422	0.85[EUR][1000 genomes]
rs17001424	0.85[EUR][1000 genomes]
rs17001433	0.85[EUR][1000 genomes]
rs17506007	1.00[ASW][hapmap]
rs2276886	1.00[LWK][hapmap]
rs33997696	0.85[EUR][1000 genomes]
rs34747816	0.85[EUR][1000 genomes]
rs4129780	0.80[MKK][hapmap]
rs41349449	1.00[ASW][hapmap];0.89[CEU][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs41411447	1.00[ASW][hapmap];0.89[CEU][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs41498548	1.00[ASW][hapmap];0.80[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4241591	1.00[JPT][hapmap]
rs4308383	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs4403073	0.85[EUR][1000 genomes]
rs4408983	0.85[EUR][1000 genomes]
rs4597859	1.00[ASW][hapmap];0.83[TSI][hapmap]
rs4624679	1.00[JPT][hapmap]
rs56669417	0.85[EUR][1000 genomes]
rs56670659	0.85[EUR][1000 genomes]
rs56788469	0.85[EUR][1000 genomes]
rs56887664	0.85[EUR][1000 genomes]
rs57268096	0.85[EUR][1000 genomes]
rs57960366	0.85[EUR][1000 genomes]
rs58127619	0.85[EUR][1000 genomes]
rs58232272	0.92[EUR][1000 genomes]
rs58319866	0.85[EUR][1000 genomes]
rs58358710	0.84[EUR][1000 genomes]
rs58380268	0.85[EUR][1000 genomes]
rs58510808	0.82[EUR][1000 genomes]
rs59547714	0.85[EUR][1000 genomes]
rs59765882	0.85[EUR][1000 genomes]
rs59789355	0.85[EUR][1000 genomes]
rs60160936	0.84[EUR][1000 genomes]
rs60387070	0.85[EUR][1000 genomes]
rs60573877	0.85[EUR][1000 genomes]
rs60610578	0.85[EUR][1000 genomes]
rs61099048	0.85[EUR][1000 genomes]
rs61293119	0.85[EUR][1000 genomes]
rs61369069	0.85[EUR][1000 genomes]
rs61391079	0.84[EUR][1000 genomes]
rs61693363	0.85[EUR][1000 genomes]
rs62299341	0.85[EUR][1000 genomes]
rs62299342	0.85[EUR][1000 genomes]
rs62299348	0.85[EUR][1000 genomes]
rs62299349	0.84[EUR][1000 genomes]
rs62299350	0.84[EUR][1000 genomes]
rs62299354	0.85[EUR][1000 genomes]
rs62299355	0.85[EUR][1000 genomes]
rs62318915	0.92[EUR][1000 genomes]
rs62318925	0.85[EUR][1000 genomes]
rs62318926	0.85[EUR][1000 genomes]
rs62318928	0.85[EUR][1000 genomes]
rs62318929	0.85[EUR][1000 genomes]
rs6532056	1.00[ASN][1000 genomes]
rs6532201	0.85[EUR][1000 genomes]
rs6813732	0.85[EUR][1000 genomes]
rs6836703	0.85[EUR][1000 genomes]
rs6836715	0.85[EUR][1000 genomes]
rs6838303	0.85[EUR][1000 genomes]
rs6838328	0.85[EUR][1000 genomes]
rs6840007	0.85[EUR][1000 genomes]
rs6843361	0.85[EUR][1000 genomes]
rs7656282	0.85[EUR][1000 genomes]
rs7656734	0.87[EUR][1000 genomes]
rs7656736	1.00[ASN][1000 genomes]
rs7657846	1.00[ASW][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7661431	0.85[EUR][1000 genomes]
rs7662240	0.85[EUR][1000 genomes]
rs7664821	0.85[EUR][1000 genomes]
rs7666848	0.85[EUR][1000 genomes]
rs7667810	1.00[ASW][hapmap];0.83[TSI][hapmap]
rs7668507	0.85[EUR][1000 genomes]
rs7670483	0.92[EUR][1000 genomes]
rs7675107	0.85[EUR][1000 genomes]
rs7675618	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs7679084	0.85[EUR][1000 genomes]
rs7679283	0.85[EUR][1000 genomes]
rs7679611	0.85[EUR][1000 genomes]
rs7690763	0.85[EUR][1000 genomes]
rs7692789	0.85[EUR][1000 genomes]
rs7693762	0.85[EUR][1000 genomes]
rs7695601	0.85[EUR][1000 genomes]
rs7697701	0.85[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17224545	NUP54	cis	Thyroid	GTEx
rs17224545	CDKL2	cis	cerebellum	SCAN
rs17224545	NUP54	cis	parietal	SCAN
rs17224545	NUP54	cis	Nerve Tibial	GTEx
rs17224545	NUP54	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77017000-77034400	Weak transcription	Right Ventricle	heart
2	chr4:77021200-77026600	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:77024000-77032200	Weak transcription	Left Ventricle	heart
4	chr4:77024800-77027000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:77025400-77026200	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:77025800-77026000	Enhancers	K562	blood
7	chr4:77025800-77026400	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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