Variant report

Variant	rs12714149
Chromosome Location	chr2:85898898-85898899
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1030862	0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs13011848	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13012309	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1436968	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1866140	1.00[ASW][hapmap]
rs2077079	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3024798	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4616480	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547631	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs934773	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs934774	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874464	chr2:85886175-85898898	Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv874465	chr2:85898898-85939207	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12714149	GGCX	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85883600-85900000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:85886400-85901000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:85887000-85905800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:85891000-85905800	Weak transcription	Right Atrium	heart
5	chr2:85893000-85899200	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr2:85893000-85903000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:85894000-85905000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:85895600-85900800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:85896200-85901200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:85896400-85900600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:85896600-85900600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:85896600-85901200	Weak transcription	Lung	lung
13	chr2:85897200-85900000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:85897200-85905600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:85897800-85899800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr2:85898800-85900000	Enhancers	Primary B cells from cord blood	blood

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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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