Variant report

Variant	rs240469
Chromosome Location	chr21:17760287-17760288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1449522	0.81[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs171267	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1964483	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2044734	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs240471	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs240476	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240478	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240479	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs240482	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28463025	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064857	chr21:17628760-18533131	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
2	nsv544382	chr21:17628760-18533131	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
3	nsv913416	chr21:17728224-17863882	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs240469	SP110	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17735800-17767200	Weak transcription	Fetal Muscle Leg	muscle
2	chr21:17742800-17760800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:17745200-17764000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr21:17751200-17760600	Weak transcription	Ovary	ovary
5	chr21:17751600-17760800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr21:17752800-17763200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:17759200-17760800	Weak transcription	Fetal Heart	heart
8	chr21:17759400-17762000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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Input of quick search could be:

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

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