Variant report

Variant	rs10239000
Chromosome Location	chr7:50332196-50332197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2012508	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085422	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2085423	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4917130	0.86[EUR][1000 genomes]
rs963594	0.93[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.97[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	nsv464444	chr7:49671882-50454736	Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv606897	chr7:49671883-50454736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv498090	chr7:49708644-50427714	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1020869	chr7:49712860-50457544	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1024102	chr7:50195864-50418159	Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10239000	CDC14C	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50325000-50332200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr7:50325000-50340000	Weak transcription	Thymus	Thymus
3	chr7:50325600-50332800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:50325800-50343000	Weak transcription	K562	blood
5	chr7:50331600-50333000	Enhancers	GM12878-XiMat	blood
6	chr7:50331600-50333200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr7:50331800-50332800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr7:50331800-50334000	Enhancers	Primary B cells from cord blood	blood
9	chr7:50331800-50335800	Weak transcription	Primary T cells from cord blood	blood
10	chr7:50332000-50332400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:50332000-50334200	Enhancers	Primary B cells from peripheral blood	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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