Variant report

Variant	rs949813
Chromosome Location	chr2:39889229-39889230
allele	A/C
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	FOXA1	chr2:39888869-39889247	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TMEM178A	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10170462	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10177801	0.86[EUR][1000 genomes]
rs10186346	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10208929	0.86[EUR][1000 genomes]
rs11124689	0.86[EUR][1000 genomes]
rs12613210	0.88[EUR][1000 genomes]
rs12712652	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12989245	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13384364	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13405084	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13409487	0.97[EUR][1000 genomes]
rs1548870	0.86[EUR][1000 genomes]
rs1548871	0.86[EUR][1000 genomes]
rs17024145	0.83[CEU][hapmap]
rs1861244	1.00[CEU][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2041736	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2058618	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2160199	0.84[CEU][hapmap]
rs2215956	0.86[EUR][1000 genomes]
rs2540200	0.95[EUR][1000 genomes]
rs2540247	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2540248	0.94[EUR][1000 genomes]
rs2540249	0.94[EUR][1000 genomes]
rs2540250	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2540251	0.94[EUR][1000 genomes]
rs2540252	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2540255	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2716682	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716683	0.88[EUR][1000 genomes]
rs2716684	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2716686	0.95[EUR][1000 genomes]
rs2716687	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2716688	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2716690	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716691	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716692	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716693	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716694	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2716719	0.85[EUR][1000 genomes]
rs2716720	0.86[EUR][1000 genomes]
rs2716732	0.97[EUR][1000 genomes]
rs2716737	0.96[EUR][1000 genomes]
rs2716738	0.95[EUR][1000 genomes]
rs35791480	0.88[EUR][1000 genomes]
rs4670952	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4670954	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6707177	0.84[EUR][1000 genomes]
rs6711206	0.81[EUR][1000 genomes]
rs6736442	0.86[EUR][1000 genomes]
rs6748628	0.86[EUR][1000 genomes]
rs917964	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs949812	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39885600-39893600	Weak transcription	Fetal Brain Male	brain
2	chr2:39887200-39889400	Enhancers	HSMM	muscle
3	chr2:39887200-39890000	Enhancers	HSMMtube	muscle
4	chr2:39887800-39889800	Enhancers	NHLF	lung
5	chr2:39888000-39889600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr2:39888200-39889400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:39888200-39889400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr2:39888400-39889600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:39888400-39892400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:39888600-39889800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:39888600-39891200	Weak transcription	Fetal Brain Female	brain
12	chr2:39888600-39892000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:39888600-39892400	Weak transcription	Brain Angular Gyrus	brain
14	chr2:39888800-39889800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:39888800-39889800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:39889200-39889400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr2:39889200-39889400	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links