Variant report

Variant	rs10415940
Chromosome Location	chr19:42214914-42214915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10402825	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10407083	0.81[YRI][hapmap]
rs12461373	0.80[EUR][1000 genomes]
rs12971352	0.83[EUR][1000 genomes]
rs12979109	0.80[EUR][1000 genomes]
rs28683503	0.83[EUR][1000 genomes]
rs34155934	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35091611	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3928915	0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3928918	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3928919	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7250222	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7256221	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7256597	0.84[EUR][1000 genomes]
rs7257798	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257962	0.84[EUR][1000 genomes]
rs7258524	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7259215	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs889365	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061309	chr19:42187716-42228445	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv482220	chr19:42212530-42234436	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3425986	chr19:42212540-42259719	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10415940	CPT1C	cis	cerebellum	SCAN
rs10415940	CCDC114	cis	cerebellum	SCAN
rs10415940	PPM1N	cis	parietal	SCAN
rs10415940	CRX	cis	cerebellum	SCAN
rs10415940	NUCB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42212000-42216200	Active TSS	Esophagus	oesophagus
2	chr19:42212000-42222800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:42212600-42215200	Active TSS	Fetal Intestine Small	intestine
4	chr19:42213000-42215000	Active TSS	Fetal Stomach	stomach
5	chr19:42213600-42217200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
6	chr19:42213800-42216600	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
7	chr19:42213800-42216600	Transcr. at gene 5' and 3'	Sigmoid Colon	Sigmoid Colon
8	chr19:42214000-42217000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
9	chr19:42214400-42215000	Weak transcription	Stomach Mucosa	stomach
10	chr19:42214600-42216400	Active TSS	Small Intestine	intestine
11	chr19:42214600-42216600	Active TSS	Rectal Smooth Muscle	rectum

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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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