Variant report

Variant	rs3893392
Chromosome Location	chr20:12987789-12987790
allele	A/G
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	MYC	chr20:12987484-12987958	MCF10A-Er-Src	breast:	n/a	chr20:12987690-12987699
2	FOS	chr20:12987469-12987939	MCF10A-Er-Src	breast:	n/a	chr20:12987794-12987806 chr20:12987689-12987701 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987691-12987700
3	STAT3	chr20:12987260-12987992	MCF10A-Er-Src	breast:	n/a	chr20:12987835-12987849 chr20:12987691-12987700 chr20:12987836-12987847
4	FOS	chr20:12987440-12987969	MCF10A-Er-Src	breast:	n/a	chr20:12987794-12987806 chr20:12987689-12987701 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987691-12987700
5	POLR2A	chr20:12987771-12987928	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr20:12987314-12987987	MCF10A-Er-Src	breast:	n/a	chr20:12987794-12987806 chr20:12987689-12987701 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987691-12987700
7	CEBPB	chr20:12987377-12987955	A549	lung:	n/a	chr20:12987578-12987591
8	FOSL2	chr20:12987480-12987953	A549	lung:	n/a	chr20:12987794-12987806 chr20:12987689-12987701 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987691-12987700
9	STAT3	chr20:12987402-12988126	MCF10A-Er-Src	breast:	n/a	chr20:12987835-12987849 chr20:12987691-12987700 chr20:12987836-12987847
10	STAT3	chr20:12987499-12988079	MCF10A-Er-Src	breast:	n/a	chr20:12987835-12987849 chr20:12987691-12987700 chr20:12987836-12987847
11	CEBPB	chr20:12987439-12987889	Hela-S3	cervix:	n/a	chr20:12987578-12987591
12	STAT3	chr20:12987508-12988031	MCF10A-Er-Src	breast:	n/a	chr20:12987835-12987849 chr20:12987691-12987700 chr20:12987836-12987847
13	JUND	chr20:12987505-12987921	Hela-S3	cervix:	n/a	chr20:12987794-12987806 chr20:12987689-12987700 chr20:12987689-12987701 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987691-12987700
14	JUND	chr20:12987514-12987874	HepG2	liver:	n/a	chr20:12987794-12987806 chr20:12987689-12987700 chr20:12987689-12987701 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987691-12987700
15	CEBPB	chr20:12987387-12987985	IMR90	lung:	n/a	chr20:12987578-12987591
16	CEBPB	chr20:12987446-12987873	HepG2	liver:	n/a	chr20:12987578-12987591
17	JUN	chr20:12987576-12987869	HepG2	liver:	n/a	chr20:12987794-12987806 chr20:12987689-12987701 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987691-12987700
18	MYC	chr20:12987470-12987939	MCF10A-Er-Src	breast:	n/a	chr20:12987690-12987699
19	FOS	chr20:12987417-12988030	MCF10A-Er-Src	breast:	n/a	chr20:12987794-12987806 chr20:12987689-12987701 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987690-12987700 chr20:12987691-12987700
20	CEBPB	chr20:12987506-12987870	A549	lung:	n/a	chr20:12987578-12987591
21	E2F4	chr20:12987651-12987957	MCF10A-Er-Src	breast:	n/a	n/a
22	EP300	chr20:12987519-12987864	Hela-S3	cervix:	n/a	chr20:12987690-12987699
23	POLR2A	chr20:12987461-12987950	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SPTLC3	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1594473	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs181716	0.83[EUR][1000 genomes]
rs3848760	0.84[ASN][1000 genomes]
rs3848761	0.84[ASN][1000 genomes]
rs3848762	0.83[LWK][hapmap]
rs3887985	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3889156	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3906635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3966739	0.83[LWK][hapmap]
rs418264	0.83[EUR][1000 genomes]
rs4813103	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4813106	0.89[CHD][hapmap];0.81[JPT][hapmap]
rs4814179	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033570	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6041762	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6078879	0.98[ASN][1000 genomes]
rs6131421	0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833923	chr20:12904689-13064426	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12981200-12988400	Weak transcription	Fetal Intestine Small	intestine
2	chr20:12982800-12989400	Weak transcription	Fetal Intestine Large	intestine
3	chr20:12984800-12989600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:12986800-12989200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:12986800-12989200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr20:12987000-12987800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr20:12987000-12988600	Enhancers	HMEC	breast
8	chr20:12987000-12989200	Enhancers	Placenta	Placenta
9	chr20:12987000-12989200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr20:12987000-12989200	Enhancers	NHEK	skin
11	chr20:12987000-12989200	Enhancers	Osteobl	bone
12	chr20:12987000-12989400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:12987200-12987800	Enhancers	A549	lung
14	chr20:12987200-12987800	Enhancers	HSMM	muscle
15	chr20:12987200-12987800	Enhancers	HSMMtube	muscle
16	chr20:12987200-12987800	Enhancers	NHLF	lung
17	chr20:12987200-12988000	Enhancers	Hela-S3	cervix
18	chr20:12987200-12989600	Enhancers	Liver	Liver
19	chr20:12987400-12988000	Enhancers	HepG2	liver
20	chr20:12987400-12988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr20:12987400-12989400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:12987600-12989400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:12987600-12989400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:12987600-12989600	Weak transcription	Monocytes-CD14+_RO01746	blood

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