Variant report

Variant	rs6450430
Chromosome Location	chr5:56982315-56982316
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:56977051..56979495-chr5:56982017..56985832,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPBP1-7	chr5:56982202-56982343	l_2923_chr5:56982201-57002577_liver

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10069403	0.81[EUR][1000 genomes]
rs10077005	0.91[EUR][1000 genomes]
rs10487613	0.99[EUR][1000 genomes]
rs10487614	0.97[EUR][1000 genomes]
rs10940569	0.87[EUR][1000 genomes]
rs10940570	0.85[EUR][1000 genomes]
rs11738377	0.87[EUR][1000 genomes]
rs11738862	0.88[EUR][1000 genomes]
rs11740506	0.87[EUR][1000 genomes]
rs11742166	0.87[EUR][1000 genomes]
rs12153161	0.87[EUR][1000 genomes]
rs12652614	0.87[EUR][1000 genomes]
rs13161204	0.87[EUR][1000 genomes]
rs13177900	0.87[EUR][1000 genomes]
rs13185580	0.90[EUR][1000 genomes]
rs13360093	0.81[ASN][1000 genomes]
rs1476831	0.87[EUR][1000 genomes]
rs1476832	0.87[EUR][1000 genomes]
rs170740	0.97[EUR][1000 genomes]
rs183477	0.97[EUR][1000 genomes]
rs2017201	0.90[EUR][1000 genomes]
rs2041678	0.87[EUR][1000 genomes]
rs2191445	0.90[EUR][1000 genomes]
rs2191446	0.90[EUR][1000 genomes]
rs2191448	0.90[EUR][1000 genomes]
rs2191449	0.87[EUR][1000 genomes]
rs2215420	0.98[EUR][1000 genomes]
rs2215421	0.86[EUR][1000 genomes]
rs229960	0.82[EUR][1000 genomes]
rs229961	0.80[EUR][1000 genomes]
rs229963	0.82[EUR][1000 genomes]
rs229965	0.82[EUR][1000 genomes]
rs230823	0.85[EUR][1000 genomes]
rs230824	0.85[EUR][1000 genomes]
rs230825	0.85[EUR][1000 genomes]
rs230826	0.85[EUR][1000 genomes]
rs230827	0.84[EUR][1000 genomes]
rs230846	0.98[EUR][1000 genomes]
rs230847	0.86[EUR][1000 genomes]
rs230848	0.86[EUR][1000 genomes]
rs230849	0.86[EUR][1000 genomes]
rs230850	0.86[EUR][1000 genomes]
rs230851	0.86[EUR][1000 genomes]
rs230852	0.86[EUR][1000 genomes]
rs230853	0.96[EUR][1000 genomes]
rs230854	0.87[EUR][1000 genomes]
rs230855	0.87[EUR][1000 genomes]
rs230856	0.87[EUR][1000 genomes]
rs230857	0.87[EUR][1000 genomes]
rs230858	0.87[EUR][1000 genomes]
rs230859	0.87[EUR][1000 genomes]
rs230860	0.98[EUR][1000 genomes]
rs230861	0.98[EUR][1000 genomes]
rs2408846	0.90[EUR][1000 genomes]
rs2408849	0.86[EUR][1000 genomes]
rs2898028	0.86[EUR][1000 genomes]
rs4141128	0.85[EUR][1000 genomes]
rs4235474	0.98[EUR][1000 genomes]
rs4699909	0.87[EUR][1000 genomes]
rs4699910	0.90[EUR][1000 genomes]
rs4700210	0.87[EUR][1000 genomes]
rs4700211	0.87[EUR][1000 genomes]
rs4700214	0.90[EUR][1000 genomes]
rs55836829	0.81[ASN][1000 genomes]
rs6450431	0.91[EUR][1000 genomes]
rs6886241	0.99[EUR][1000 genomes]
rs702695	0.86[EUR][1000 genomes]
rs702696	0.86[EUR][1000 genomes]
rs7714534	0.87[EUR][1000 genomes]
rs7719947	0.87[EUR][1000 genomes]
rs7726732	0.99[EUR][1000 genomes]
rs7732108	0.90[EUR][1000 genomes]
rs7737409	0.90[EUR][1000 genomes]
rs854137	0.86[EUR][1000 genomes]
rs887503	0.87[EUR][1000 genomes]
rs917655	0.98[EUR][1000 genomes]
rs986101	0.90[EUR][1000 genomes]
rs991727	0.90[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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6450430	CDC20B	cis	cerebellum	SCAN
rs6450430	TADA2B	trans	parietal	SCAN
rs6450430	GZMK	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56972400-56988400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:56978800-56983600	Weak transcription	NHEK	skin
3	chr5:56979400-56983600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:56979600-56986800	Weak transcription	K562	blood
5	chr5:56979600-56987000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:56979800-56983600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:56980400-56987200	Weak transcription	Ovary	ovary
8	chr5:56980600-56983600	Weak transcription	HMEC	breast
9	chr5:56981200-56983600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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