Variant report

Variant	rs10916142
Chromosome Location	chr1:227603016-227603017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10916134	0.88[GIH][hapmap]
rs12028062	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12030200	0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12047468	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs3014268	0.88[GIH][hapmap]
rs6426453	0.88[AMR][1000 genomes]
rs72764709	0.84[AMR][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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv873243	chr1:227581017-227617519	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10916142	PSEN2	cis	cerebellum	SCAN
rs10916142	CAPN2	cis	parietal	SCAN
rs10916142	WNT9A	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227599200-227603200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:227602600-227604000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:227602800-227603400	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:227602800-227603800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:227602800-227604000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:227602800-227604600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:227603000-227603200	Enhancers	Left Ventricle	heart
8	chr1:227603000-227604200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:227603000-227604600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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