Variant report

Variant	rs17242584
Chromosome Location	chr5:52536387-52536388
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52532240..52534104-chr5:52535420..52537788,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10065796	0.93[GIH][hapmap];0.89[MEX][hapmap]
rs10067414	0.81[EUR][1000 genomes]
rs10067418	0.81[EUR][1000 genomes]
rs10940304	0.81[EUR][1000 genomes]
rs10940308	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11740027	0.80[EUR][1000 genomes]
rs12517334	0.87[EUR][1000 genomes]
rs12520159	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1318732	0.87[EUR][1000 genomes]
rs1374052	0.81[EUR][1000 genomes]
rs1374053	0.81[EUR][1000 genomes]
rs1374054	0.81[EUR][1000 genomes]
rs1445985	0.81[EUR][1000 genomes]
rs1549247	0.81[EUR][1000 genomes]
rs16881173	0.87[EUR][1000 genomes]
rs16881189	0.84[EUR][1000 genomes]
rs17241927	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1813600	0.87[EUR][1000 genomes]
rs1816904	0.81[EUR][1000 genomes]
rs1960785	0.85[EUR][1000 genomes]
rs1960786	0.86[EUR][1000 genomes]
rs2112876	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2406615	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2406617	0.87[EUR][1000 genomes]
rs38058	0.87[ASW][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs4361475	0.81[EUR][1000 genomes]
rs56296560	0.84[EUR][1000 genomes]
rs56909170	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58049370	0.81[EUR][1000 genomes]
rs61388559	0.81[EUR][1000 genomes]
rs62357405	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62357407	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62357430	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62357442	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6450115	0.81[EUR][1000 genomes]
rs6450116	0.80[EUR][1000 genomes]
rs6450117	0.81[EUR][1000 genomes]
rs6450120	0.81[EUR][1000 genomes]
rs6450121	0.81[EUR][1000 genomes]
rs6450122	0.81[EUR][1000 genomes]
rs6866517	0.81[EUR][1000 genomes]
rs6870259	0.81[EUR][1000 genomes]
rs6872591	0.81[EUR][1000 genomes]
rs6876789	0.81[EUR][1000 genomes]
rs6882524	0.81[EUR][1000 genomes]
rs6885965	0.81[EUR][1000 genomes]
rs6892815	0.81[EUR][1000 genomes]
rs6896855	0.81[EUR][1000 genomes]
rs6897000	0.81[EUR][1000 genomes]
rs6897965	0.81[EUR][1000 genomes]
rs6898261	0.81[EUR][1000 genomes]
rs6898901	0.81[EUR][1000 genomes]
rs72762377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs731383	0.81[EUR][1000 genomes]
rs733420	0.81[EUR][1000 genomes]
rs733421	0.81[EUR][1000 genomes]
rs7704622	0.81[EUR][1000 genomes]
rs7705771	0.81[EUR][1000 genomes]
rs7707051	0.81[EUR][1000 genomes]
rs7720876	0.80[EUR][1000 genomes]
rs7721172	0.81[EUR][1000 genomes]
rs7734784	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv830297	chr5:52492494-52707758	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv515913	chr5:52492677-52545841	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv522454	chr5:52492677-52571758	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv880833	chr5:52502168-52544231	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17242584	CDC20B	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52509600-52540000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:52530200-52540000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:52534200-52540600	Weak transcription	HSMM	muscle
4	chr5:52535000-52536600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:52535000-52536600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:52535400-52536800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:52535400-52536800	Enhancers	NHLF	lung
8	chr5:52535600-52539200	Weak transcription	HMEC	breast
9	chr5:52535600-52539800	Weak transcription	NHDF-Ad	bronchial
10	chr5:52535600-52540600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:52535600-52540600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:52535600-52540600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:52535600-52541200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:52535800-52540600	Weak transcription	NHEK	skin
15	chr5:52535800-52540600	Weak transcription	Osteobl	bone
16	chr5:52535800-52541200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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