Variant report

Variant	rs12139441
Chromosome Location	chr1:241728198-241728199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1053221	0.82[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10926521	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10926523	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12030098	0.82[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12128430	0.82[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12138459	0.86[MKK][hapmap]
rs12144172	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3007744	1.00[ASW][hapmap]
rs3193688	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3765807	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7349139	0.83[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS 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	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12139441	WDR64	cis	parietal	SCAN
rs12139441	ATP8B2	cis	Temporal Cortex	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241714600-241732600	Weak transcription	Spleen	Spleen
2	chr1:241715800-241739400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:241716200-241746200	Weak transcription	GM12878-XiMat	blood
4	chr1:241721200-241739400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr1:241724400-241731400	Strong transcription	Primary B cells from cord blood	blood
6	chr1:241724800-241730800	Strong transcription	Liver	Liver
7	chr1:241725400-241730800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:241726200-241728800	Weak transcription	Placenta	Placenta
9	chr1:241726200-241741200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:241727800-241730600	Strong transcription	Primary monocytes fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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