Variant report

Variant	rs10406151
Chromosome Location	chr19:52680410-52680411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs17835885	0.82[CHB][hapmap]
rs2059809	0.80[ASW][hapmap];0.91[CEU][hapmap];0.84[CHB][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2059810	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4331429	0.93[ASW][hapmap];0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8107878	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv580007	chr19:52660279-52693277	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10406151	SYT5	cis	cerebellum	SCAN
rs10406151	RDH13	cis	parietal	SCAN
rs10406151	ZNF582	cis	parietal	SCAN
rs10406151	PPP1R12C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52675400-52683200	Weak transcription	Right Ventricle	heart
2	chr19:52675600-52681000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr19:52676000-52681000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:52677800-52685600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:52679000-52680600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:52679200-52680600	Enhancers	Placenta	Placenta
7	chr19:52679600-52680600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:52679800-52681200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr19:52680000-52680600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:52680000-52681200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr19:52680200-52692200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:52680400-52691800	Weak transcription	Placenta Amnion	Placenta Amnion

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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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