Variant report

Variant	rs12056089
Chromosome Location	chr7:137399820-137399821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1019583	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10234581	0.91[CHB][hapmap]
rs1025087	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12707364	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12707367	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12707372	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13234743	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1345918	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1424370	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1424371	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1424372	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1834143	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1991084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113428	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs270893	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs270894	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs270896	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2882781	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3778797	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3778799	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800624	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs3800626	0.86[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs3800628	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3800630	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800636	0.87[CHB][hapmap];0.81[CHD][hapmap];0.90[ASN][1000 genomes]
rs3800637	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3800644	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3823552	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4728420	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4732263	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4732264	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6944527	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs6957797	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6971978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6976725	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7457119	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs7806658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7806810	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9784934	0.86[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022793	chr7:137187383-137619359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv464731	chr7:137356651-137404781	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv608466	chr7:137356651-137404781	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12056089	ADCK2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137390000-137400000	Weak transcription	HSMM	muscle
2	chr7:137394400-137400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:137396400-137400600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:137396400-137400600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:137396400-137400800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:137399200-137400800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:137399200-137401200	Enhancers	Osteobl	bone
8	chr7:137399200-137403200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:137399400-137403600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:137399600-137400800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:137399600-137401800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:137399600-137402600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:137399800-137400800	Enhancers	NHDF-Ad	bronchial
14	chr7:137399800-137403200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links