Variant report

Variant	rs10873219
Chromosome Location	chr14:25101706-25101707
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10148494	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs10909625	0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap]
rs1126639	0.85[EUR][1000 genomes]
rs11539752	0.84[EUR][1000 genomes]
rs11624634	0.81[EUR][1000 genomes]
rs2236337	0.84[EUR][1000 genomes]
rs2236338	0.80[GIH][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2273843	0.91[ASN][1000 genomes]
rs2273844	0.81[JPT][hapmap];0.93[MEX][hapmap];0.84[EUR][1000 genomes]
rs6573910	0.80[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.84[EUR][1000 genomes]
rs6573911	0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs71405867	0.89[ASN][1000 genomes]
rs8192917	0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.84[EUR][1000 genomes]
rs8192919	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9671454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv1843155	chr14:25099980-25110067	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10873219	EDDM3A	cis	cerebellum	SCAN
rs10873219	SDR39U1	cis	cerebellum	SCAN
rs10873219	MDP1	cis	parietal	SCAN
rs10873219	CTSG	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25099400-25102200	Enhancers	Fetal Intestine Small	intestine
2	chr14:25099800-25102000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr14:25100200-25102600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
4	chr14:25100600-25101800	Weak transcription	Fetal Intestine Large	intestine
5	chr14:25100800-25101800	Weak transcription	Fetal Muscle Leg	muscle
6	chr14:25100800-25101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:25100800-25102000	Active TSS	Primary T cells fromperipheralblood	blood
8	chr14:25100800-25109600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr14:25101000-25101800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr14:25101200-25103600	Enhancers	Fetal Thymus	thymus
11	chr14:25101200-25112800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:25101600-25101800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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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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