Variant report

Variant	rs454187
Chromosome Location	chr6:164471824-164471825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:164445952..164448558-chr6:164471088..164472960,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1007176	0.99[ASN][1000 genomes]
rs1010549	0.99[ASN][1000 genomes]
rs16896061	0.94[ASN][1000 genomes]
rs183275	0.82[JPT][hapmap]
rs2064792	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064793	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs206696	0.99[ASN][1000 genomes]
rs206729	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2070284	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070285	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2070286	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070287	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2874705	0.99[ASN][1000 genomes]
rs368330	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs381500	0.98[ASN][1000 genomes]
rs3846781	0.99[ASN][1000 genomes]
rs415182	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421640	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs437702	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs438716	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs446073	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4709032	0.96[ASN][1000 genomes]
rs4709033	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4709034	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4709035	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4709036	0.82[ASN][1000 genomes]
rs4709818	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4709819	0.99[ASN][1000 genomes]
rs4709820	0.98[ASN][1000 genomes]
rs4709821	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62435861	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs672706	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689056	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6901582	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6905119	0.97[ASN][1000 genomes]
rs724281	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs724282	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs724283	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs736661	0.99[ASN][1000 genomes]
rs7743991	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7765982	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295254	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356181	0.97[ASN][1000 genomes]
rs9356182	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9458972	0.83[ASN][1000 genomes]
rs9458973	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription 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	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1026707	chr6:164188210-164749206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv538527	chr6:164188210-164749206	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1019703	chr6:164424683-164488780	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1029952	chr6:164463355-165268911	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs454187	HGC6.3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164471400-164473000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:164471600-164474800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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