Variant report

Variant	rs235948
Chromosome Location	chr21:28562954-28562955
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs173123	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs173124	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs235943	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs235944	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs235945	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs235946	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs235947	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs235949	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235950	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2830757	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28393903	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7278178	0.92[ASN][1000 genomes]
rs73374980	0.94[ASN][1000 genomes]
rs9636576	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9636577	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9636793	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	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv459229	chr21:28543456-29482488	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv587342	chr21:28543456-29482488	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv459231	chr21:28543715-28563495	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
5	nsv587343	chr21:28543715-28563495	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
6	nsv834070	chr21:28546745-28709950	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs235948	MIR155HG	cis	cerebellum	SCAN
rs235948	NCRNA00161	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28562200-28563800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr21:28562200-28563800	Enhancers	Hela-S3	cervix
3	chr21:28562600-28563800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr21:28562800-28563000	Enhancers	HSMM	muscle
5	chr21:28562800-28563400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr21:28562800-28563400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr21:28562800-28563600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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