Variant report

Variant	rs688749
Chromosome Location	chr11:64736404-64736405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11231913	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs240565	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240567	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs240571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240572	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518909	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670908	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35131180	0.81[EUR][1000 genomes]
rs470511	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs519796	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs594392	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs610130	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs675090	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv555208	chr11:64645119-64771179	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1029 gene(s)	inside rSNPs	diseases
3	nsv976460	chr11:64727780-64743097	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs688749	SPDYC	cis	Whole Blood	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64730200-64738400	Weak transcription	Stomach Mucosa	stomach
2	chr11:64735200-64739000	Weak transcription	GM12878-XiMat	blood
3	chr11:64736000-64739000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:64736200-64738400	Enhancers	NHEK	skin
5	chr11:64736200-64739000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:64736400-64736800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr11:64736400-64737000	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr11:64736400-64737800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:64736400-64739200	Enhancers	HMEC	breast

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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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