Variant report

Variant	rs13083244
Chromosome Location	chr3:158998151-158998152
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	GATA3	chr3:158998010-158998589	SH-SY5Y	brain:	n/a	n/a
2	STAT3	chr3:158997964-158998154	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr3:158998096-158998729	SK-N-SH_RA	brain:	n/a	n/a
4	EP300	chr3:158998008-158998646	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr3:158997659-158999016	SK-N-SH	brain:	n/a	n/a
6	GATA2	chr3:158997786-158998990	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158998052..159000120-chr3:159030298..159031893,2	K562	blood:
2	chr3:158991788..158993700-chr3:158997368..159000280,2	MCF-7	breast:

Variant related genes	Relation type
MIR3919	TF binding region

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

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11917412	1.00[CEU][hapmap]
rs11917829	0.88[CEU][hapmap]
rs11920486	0.94[CEU][hapmap]
rs12696092	1.00[CEU][hapmap]
rs13059800	0.82[CEU][hapmap]
rs13060178	0.81[CEU][hapmap]
rs13061579	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13061619	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs13063797	0.95[EUR][1000 genomes]
rs13065679	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13066122	0.94[CEU][hapmap]
rs13067585	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13070853	0.93[CEU][hapmap]
rs13071140	0.93[CEU][hapmap]
rs13072096	0.83[CEU][hapmap]
rs13075790	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13077258	1.00[CEU][hapmap]
rs13078847	0.83[CEU][hapmap]
rs13079265	0.83[CEU][hapmap]
rs13080892	0.94[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs13082502	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13083138	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13083408	0.83[CEU][hapmap]
rs13083887	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13085008	1.00[CEU][hapmap]
rs13085667	1.00[CEU][hapmap]
rs13085824	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13088547	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13091349	0.83[CEU][hapmap]
rs13095658	0.93[CEU][hapmap]
rs1448996	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1449002	0.94[CEU][hapmap]
rs17795417	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1839219	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1906951	1.00[CEU][hapmap]
rs2886480	1.00[CEU][hapmap]
rs34442071	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35150496	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4328854	0.83[CEU][hapmap]
rs61795163	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6781001	0.83[CEU][hapmap]
rs6781285	0.94[CEU][hapmap]
rs6784143	1.00[CEU][hapmap]
rs7620377	1.00[CEU][hapmap];0.83[GIH][hapmap]
rs7631740	0.94[CEU][hapmap]
rs7644770	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs870852	0.94[CEU][hapmap]
rs9848338	1.00[CEU][hapmap]
rs9848831	1.00[CEU][hapmap]
rs9968056	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158992000-158998200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:158997600-158999200	Enhancers	Brain Germinal Matrix	brain
3	chr3:158997800-158998600	Enhancers	Fetal Brain Female	brain
4	chr3:158997800-158999000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:158997800-158999200	Enhancers	Adipose Nuclei	Adipose
6	chr3:158997800-158999200	Enhancers	Fetal Brain Male	brain
7	chr3:158998000-158998800	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:158998000-158999000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links