Variant report

Variant	rs12089565
Chromosome Location	chr1:224775840-224775841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1036431	0.83[CEU][hapmap]
rs1039265	0.81[CEU][hapmap]
rs10915691	0.83[CEU][hapmap]
rs10915693	0.83[CEU][hapmap]
rs10915695	0.83[CEU][hapmap]
rs10916641	0.86[CHB][hapmap]
rs1106233	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12060334	0.83[CEU][hapmap]
rs12065840	0.83[CEU][hapmap]
rs12077707	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12079156	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12088524	0.83[CEU][hapmap]
rs12091093	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565092	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1337538	0.91[CEU][hapmap]
rs1499289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1499291	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1499293	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1532557	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16850786	0.83[CEU][hapmap]
rs1985338	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4363402	0.83[CEU][hapmap]
rs58725094	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60500269	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827075	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61827076	0.90[EUR][1000 genomes]
rs6426147	0.83[CEU][hapmap]
rs6695864	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73115953	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73115958	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7415393	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7554310	0.83[CEU][hapmap]
rs883116	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs969025	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv873224	chr1:224746577-224794913	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224753600-224780400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:224767400-224779600	Weak transcription	HMEC	breast
3	chr1:224767600-224779800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:224767800-224780200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:224768000-224776400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:224768000-224776600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:224768000-224776800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:224768000-224780400	Weak transcription	Psoas Muscle	Psoas
9	chr1:224768800-224779600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:224770000-224776000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:224770200-224776000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:224775800-224777000	Enhancers	Fetal Brain Male	brain
13	chr1:224775800-224777600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:224775800-224777600	Enhancers	Cortex derived primary cultured neurospheres	brain

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