Variant report

Variant	rs2332406
Chromosome Location	chr14:25079343-25079344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1033810	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158812	0.98[ASN][1000 genomes]
rs12590828	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1951593	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1951595	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1957525	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2093498	0.88[CEU][hapmap]
rs4982970	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7144488	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7160134	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72681022	1.00[ASN][1000 genomes]
rs8004747	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8014501	0.86[EUR][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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv510631	chr14:25045183-25172311	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv901502	chr14:25074711-25101706	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2332406	SDR39U1	cis	lymphoblastoid	seeQTL
rs2332406	RNASE3	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25076200-25081600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr14:25077200-25081200	Weak transcription	Spleen	Spleen
3	chr14:25077400-25082200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr14:25078200-25079800	Enhancers	GM12878-XiMat	blood
5	chr14:25078400-25092200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr14:25078600-25081200	Weak transcription	Fetal Intestine Large	intestine
7	chr14:25078800-25081200	Weak transcription	Fetal Intestine Small	intestine
8	chr14:25079000-25079400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr14:25079000-25080000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr14:25079000-25080400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr14:25079000-25081200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr14:25079200-25079600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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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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