Variant report

Variant	rs12457781
Chromosome Location	chr18:25678656-25678657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr18:25678115-25678675	U2OS	brain:	n/a	n/a
2	POLR2A	chr18:25678459-25678667	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CDH2	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10853682	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083249	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083250	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083252	1.00[JPT][hapmap]
rs11564299	1.00[JPT][hapmap]
rs11564310	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11564336	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11564341	1.00[JPT][hapmap]
rs11564381	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11872284	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11874384	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11874478	1.00[JPT][hapmap]
rs12185349	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453985	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12454164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12454769	1.00[ASN][1000 genomes]
rs12457737	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12458418	1.00[JPT][hapmap]
rs12458840	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12458872	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12953509	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956036	1.00[JPT][hapmap]
rs12959867	1.00[JPT][hapmap]
rs12960181	1.00[JPT][hapmap]
rs12969129	1.00[ASN][1000 genomes]
rs1443449	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17446505	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17446547	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17446875	1.00[JPT][hapmap]
rs17468924	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17468987	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17469001	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17469371	1.00[JPT][hapmap]
rs17536472	1.00[JPT][hapmap]
rs1860642	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1944288	1.00[JPT][hapmap]
rs2067772	0.95[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191636	1.00[JPT][hapmap]
rs4800289	1.00[JPT][hapmap]
rs4800842	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508526	1.00[JPT][hapmap]
rs719723	1.00[JPT][hapmap]
rs8089347	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091862	1.00[JPT][hapmap]
rs8095341	1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25655800-25690800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:25668000-25680200	Weak transcription	HSMM	muscle
3	chr18:25668200-25688000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr18:25670400-25687800	Weak transcription	Brain Germinal Matrix	brain
5	chr18:25670600-25690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:25672000-25688000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr18:25672200-25680000	Weak transcription	Left Ventricle	heart
8	chr18:25672200-25680200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr18:25673000-25688400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr18:25673600-25687400	Weak transcription	HepG2	liver
11	chr18:25674200-25679800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:25675200-25688400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr18:25676000-25685000	Weak transcription	NH-A	brain
14	chr18:25676200-25688400	Weak transcription	Osteobl	bone
15	chr18:25677000-25681600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:25677200-25687200	Weak transcription	Fetal Brain Female	brain
17	chr18:25678200-25678800	ZNF genes & repeats	Liver	Liver
18	chr18:25678200-25685200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:25678400-25678800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:25678400-25678800	ZNF genes & repeats	Fetal Heart	heart
21	chr18:25678400-25679000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links