Variant report

Variant	rs1401406
Chromosome Location	chr3:56080342-56080343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12637898	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222248	0.81[EUR][1000 genomes]
rs61532273	0.81[EUR][1000 genomes]
rs6445765	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6772984	0.99[EUR][1000 genomes]
rs6795659	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6803094	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7636594	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9819904	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56071000-56084600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:56076400-56080600	Weak transcription	Fetal Kidney	kidney
3	chr3:56076400-56086400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:56076600-56082800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:56076600-56086200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:56078000-56086200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:56078400-56082600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:56078600-56082600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:56079400-56080800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:56079600-56086200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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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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