Variant report

Variant	rs5997780
Chromosome Location	chr22:31234009-31234010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs4820908	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5994350	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5997785	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs738373	0.83[ASN][1000 genomes]
rs738374	0.89[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs8137925	0.82[ASN][1000 genomes]
rs926341	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9680690	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv588888	chr22:31212641-31249333	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv522377	chr22:31232074-31249333	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv914973	chr22:31232074-31264281	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5997780	SF3A1	cis	parietal	SCAN
rs5997780	SEZ6L	cis	cerebellum	SCAN
rs5997780	TBC1D10A	cis	parietal	SCAN
rs5997780	CHEK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31229400-31238800	Weak transcription	HSMM	muscle
2	chr22:31231800-31234400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr22:31232400-31234400	Enhancers	Brain Cingulate Gyrus	brain
4	chr22:31232400-31234600	Enhancers	Placenta	Placenta
5	chr22:31232400-31234600	Genic enhancers	NHEK	skin
6	chr22:31232600-31234400	Enhancers	Brain Angular Gyrus	brain
7	chr22:31232800-31236400	Weak transcription	Brain Anterior Caudate	brain
8	chr22:31233400-31234200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr22:31233400-31234200	Enhancers	Esophagus	oesophagus
10	chr22:31233600-31234400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr22:31233600-31234400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr22:31233600-31234400	Enhancers	HMEC	breast
13	chr22:31233600-31234600	ZNF genes & repeats	Hela-S3	cervix
14	chr22:31233600-31234600	Enhancers	NHDF-Ad	bronchial
15	chr22:31233800-31237400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr22:31234000-31236400	Weak transcription	A549	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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