Variant report

Variant	rs13084656
Chromosome Location	chr3:46280194-46280195
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13081845	0.97[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]
rs4683198	0.89[ASN][1000 genomes]
rs6441950	0.90[JPT][hapmap]
rs6441953	0.89[ASN][1000 genomes]
rs6441963	0.85[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs6793850	0.83[AFR][1000 genomes];0.96[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];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852052	0.80[ASN][1000 genomes]
rs9853223	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]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13084656	SS18L2	cis	parietal	SCAN
rs13084656	C3orf54	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46278400-46282600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr3:46278400-46283600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:46278600-46281000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:46278600-46281800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:46278600-46282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:46278600-46282800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:46278600-46283400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:46278600-46283400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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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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