Variant report

Variant	rs17001364
Chromosome Location	chr4:77009342-77009343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76982557..76984766-chr4:77008579..77010146,2	K562	blood:
2	chr4:76910404..76912093-chr4:77009234..77010931,2	MCF-7	breast:
3	chr4:77006287..77011420-chr4:77011515..77015802,5	K562	blood:
4	chr4:76931634..76933510-chr4:77007552..77010198,2	K562	blood:

Variant related genes	Relation type
ENSG00000156219	Chromatin interaction
ENSG00000198301	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10518144	0.85[ASN][1000 genomes]
rs10654	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11097244	0.80[ASN][1000 genomes]
rs1127695	0.85[ASN][1000 genomes]
rs11558468	0.80[ASN][1000 genomes]
rs11558469	0.80[ASN][1000 genomes]
rs11722957	0.85[CHB][hapmap]
rs11724260	0.85[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs11725016	0.80[ASN][1000 genomes]
rs11725358	0.82[ASN][1000 genomes]
rs11726372	0.83[ASN][1000 genomes]
rs11727718	0.84[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11729637	0.82[ASN][1000 genomes]
rs11729695	0.80[ASN][1000 genomes]
rs11729776	0.80[ASN][1000 genomes]
rs11729810	0.85[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs11733489	0.82[ASN][1000 genomes]
rs11736405	0.83[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11938770	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs12651516	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13134119	0.86[CEU][hapmap]
rs1465920	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs17001390	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17001422	0.83[ASN][1000 genomes]
rs17001424	0.85[ASN][1000 genomes]
rs17001433	0.85[ASN][1000 genomes]
rs17001532	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs17001533	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs17224545	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs28479255	0.80[ASN][1000 genomes]
rs33997696	0.85[ASN][1000 genomes]
rs34747816	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35040945	0.80[ASN][1000 genomes]
rs4129780	0.83[CHB][hapmap]
rs41349449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41411447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41498548	0.83[ASN][1000 genomes]
rs4241582	0.87[JPT][hapmap]
rs4241587	0.87[JPT][hapmap]
rs4256246	0.83[CHB][hapmap]
rs4267762	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs4308383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403073	0.85[ASN][1000 genomes]
rs4408983	0.85[ASN][1000 genomes]
rs4481255	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs4597859	0.80[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs4599438	0.88[JPT][hapmap]
rs4604075	0.80[ASN][1000 genomes]
rs4859418	0.86[CEU][hapmap]
rs56669417	0.83[ASN][1000 genomes]
rs56670659	0.86[ASN][1000 genomes]
rs56788469	0.83[ASN][1000 genomes]
rs56887664	0.83[ASN][1000 genomes]
rs56923677	0.80[ASN][1000 genomes]
rs56985043	0.80[ASN][1000 genomes]
rs57268096	0.86[ASN][1000 genomes]
rs57313943	0.80[ASN][1000 genomes]
rs57765272	0.80[ASN][1000 genomes]
rs57960366	0.83[ASN][1000 genomes]
rs58127619	0.83[ASN][1000 genomes]
rs58232272	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58247315	0.80[ASN][1000 genomes]
rs58305323	0.80[ASN][1000 genomes]
rs58319866	0.83[ASN][1000 genomes]
rs58358710	0.82[ASN][1000 genomes]
rs58380268	0.85[ASN][1000 genomes]
rs58510808	0.85[ASN][1000 genomes]
rs58528289	0.80[ASN][1000 genomes]
rs58695482	0.80[ASN][1000 genomes]
rs58728245	0.80[ASN][1000 genomes]
rs58911257	0.80[ASN][1000 genomes]
rs59084193	0.80[ASN][1000 genomes]
rs59547714	0.86[ASN][1000 genomes]
rs59765882	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59789355	0.85[ASN][1000 genomes]
rs59927725	0.80[ASN][1000 genomes]
rs60160936	0.83[ASN][1000 genomes]
rs60387070	0.85[ASN][1000 genomes]
rs60523248	0.80[ASN][1000 genomes]
rs60573877	0.83[ASN][1000 genomes]
rs60610578	0.85[ASN][1000 genomes]
rs60675531	0.80[ASN][1000 genomes]
rs60913446	0.80[ASN][1000 genomes]
rs61099048	0.82[ASN][1000 genomes]
rs61293119	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61360019	0.80[ASN][1000 genomes]
rs61369069	0.83[ASN][1000 genomes]
rs61662067	0.80[ASN][1000 genomes]
rs61693363	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62299341	0.83[ASN][1000 genomes]
rs62299342	0.83[ASN][1000 genomes]
rs62299348	0.83[ASN][1000 genomes]
rs62299349	0.83[ASN][1000 genomes]
rs62299350	0.83[ASN][1000 genomes]
rs62299354	0.83[ASN][1000 genomes]
rs62299355	0.83[ASN][1000 genomes]
rs62300565	0.80[ASN][1000 genomes]
rs62300570	0.80[ASN][1000 genomes]
rs62300572	0.80[ASN][1000 genomes]
rs62300573	0.80[ASN][1000 genomes]
rs62300609	0.80[ASN][1000 genomes]
rs62300610	0.80[ASN][1000 genomes]
rs62300611	0.80[ASN][1000 genomes]
rs62300615	0.80[ASN][1000 genomes]
rs62300617	0.80[ASN][1000 genomes]
rs62300618	0.80[ASN][1000 genomes]
rs62300619	0.80[ASN][1000 genomes]
rs62300620	0.80[ASN][1000 genomes]
rs62300621	0.80[ASN][1000 genomes]
rs62300624	0.80[ASN][1000 genomes]
rs62300625	0.80[ASN][1000 genomes]
rs62300626	0.80[ASN][1000 genomes]
rs62300627	0.80[ASN][1000 genomes]
rs62300628	0.80[ASN][1000 genomes]
rs62300629	0.80[ASN][1000 genomes]
rs62300633	0.80[ASN][1000 genomes]
rs62318915	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62318924	0.83[ASN][1000 genomes]
rs62318925	0.85[ASN][1000 genomes]
rs62318926	0.85[ASN][1000 genomes]
rs62318928	0.85[ASN][1000 genomes]
rs62318929	0.85[ASN][1000 genomes]
rs6532201	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs6813732	0.81[ASN][1000 genomes]
rs6824251	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs6836715	0.87[ASN][1000 genomes]
rs6838303	0.87[ASN][1000 genomes]
rs6840007	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6846685	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs6848297	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs7656282	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7656734	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657846	0.85[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs7661431	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7662240	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7664821	0.85[ASN][1000 genomes]
rs7666848	0.84[ASN][1000 genomes]
rs7667810	0.85[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs7668038	0.84[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7668507	0.82[ASN][1000 genomes]
rs7670483	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7674984	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7675107	0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs7675618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679084	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7679283	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7679611	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs7686854	0.80[ASN][1000 genomes]
rs7686870	0.80[ASN][1000 genomes]
rs7688452	0.80[ASN][1000 genomes]
rs7690763	0.83[ASN][1000 genomes]
rs7692789	0.80[ASN][1000 genomes]
rs7695601	0.85[ASN][1000 genomes]
rs7696379	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7697701	0.82[ASN][1000 genomes]
rs7698392	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs894246	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs9917853	0.80[ASN][1000 genomes]
rs9917948	0.80[ASN][1000 genomes]
rs9918072	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
rs17001364	NUP54	cis	Nerve Tibial	GTEx
rs17001364	NUP54	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77008000-77009400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr4:77008000-77009400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:77008400-77011200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:77008400-77011200	Weak transcription	HMEC	breast
5	chr4:77008400-77011400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:77008400-77014200	Weak transcription	Pancreas	Pancrea
7	chr4:77008600-77010000	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr4:77008600-77010600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:77008600-77010600	Weak transcription	HUVEC	blood vessel
10	chr4:77008600-77011200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:77008600-77011200	Weak transcription	K562	blood
12	chr4:77008600-77011400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:77008600-77011600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:77008600-77011600	Weak transcription	Osteobl	bone
15	chr4:77008600-77016800	Weak transcription	Psoas Muscle	Psoas
16	chr4:77008800-77011200	Weak transcription	NHEK	skin
17	chr4:77008800-77011600	Weak transcription	Fetal Heart	heart
18	chr4:77009000-77010400	Weak transcription	Hela-S3	cervix
19	chr4:77009000-77011400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr4:77009000-77011600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:77009000-77011600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:77009200-77009400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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