Variant report

Variant	rs2064793
Chromosome Location	chr6:164456716-164456717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2064792	0.82[AMR][1000 genomes]
rs206729	0.87[JPT][hapmap]
rs2070284	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2070285	0.80[EUR][1000 genomes]
rs2070286	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2070287	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs368330	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs415182	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs421640	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs437702	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs438716	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs446073	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs454187	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4709032	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4709033	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4709035	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4709818	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs672706	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689056	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs724281	0.81[EUR][1000 genomes]
rs724282	0.81[EUR][1000 genomes]
rs724283	0.80[EUR][1000 genomes]
rs7743991	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9458973	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2064793	HGC6.3	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164443200-164459000	Weak transcription	Spleen	Spleen
2	chr6:164445000-164457400	Weak transcription	Fetal Heart	heart
3	chr6:164446400-164462800	Weak transcription	Right Atrium	heart
4	chr6:164453000-164457600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:164455600-164459200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:164456000-164457000	Weak transcription	Brain Substantia Nigra	brain
7	chr6:164456400-164458400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:164456600-164457000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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