Variant report

Variant	rs9853223
Chromosome Location	chr3:46284093-46284094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13081845	0.97[ASN][1000 genomes]
rs13084656	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096142	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1388604	0.90[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs4683198	0.89[ASN][1000 genomes]
rs6441950	0.89[JPT][hapmap]
rs6441953	0.89[ASN][1000 genomes]
rs6441963	0.85[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs6793850	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794300	0.80[ASN][1000 genomes]
rs6802288	0.87[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs71615444	0.91[ASN][1000 genomes]
rs7371987	0.90[JPT][hapmap]
rs7372094	0.80[ASN][1000 genomes]
rs9842716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852052	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9853223	C3orf54	cis	cerebellum	SCAN
rs9853223	SS18L2	cis	parietal	SCAN
rs9853223	ZNF662	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46281600-46285600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:46281600-46288600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:46281800-46284400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:46282800-46284400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:46282800-46284400	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:46283200-46284600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:46283400-46284200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:46283400-46284400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr3:46283400-46284600	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:46283600-46284200	Enhancers	Fetal Thymus	thymus
11	chr3:46283600-46284400	Enhancers	Primary T cells from cord blood	blood
12	chr3:46283600-46284400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:46283800-46284200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:46283800-46284200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:46283800-46284200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr3:46283800-46284400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr3:46283800-46284400	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr3:46283800-46284400	Enhancers	GM12878-XiMat	blood
19	chr3:46284000-46284200	Enhancers	Placenta	Placenta

Quick Search:

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

what's new

Quick links