Variant report

Variant	rs11908459
Chromosome Location	chr20:12947758-12947759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:12906070..12908369-chr20:12946069..12948002,2	MCF-7	breast:
2	chr20:12904584..12906657-chr20:12946403..12948442,2	MCF-7	breast:
3	chr20:12905518..12906454-chr20:12946845..12948133,8	MCF-7	breast:
4	chr20:12905418..12906763-chr20:12946186..12947828,17	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPTLC3-1	chr20:12947694-12947858	XLOC_013465
2	lnc-SPTLC3-1	chr20:12947694-12947858	XLOC_013465
3	lnc-SPTLC3-1	chr20:12947694-12947891	XLOC_013465
4	lnc-SPTLC3-1	chr20:12947694-12947858	NONHSAT078664
5	lnc-SPTLC3-1	chr20:12947697-12947858	NONHSAT078665
6	lnc-SPTLC3-1	chr20:12947694-12947847	NONHSAT078674

No data

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11907026	1.00[EUR][1000 genomes]
rs11907467	1.00[EUR][1000 genomes]
rs11908439	1.00[EUR][1000 genomes]
rs16993615	1.00[EUR][1000 genomes]
rs399107	1.00[EUR][1000 genomes]
rs473182	1.00[EUR][1000 genomes]
rs57062041	1.00[AMR][1000 genomes]
rs57778903	1.00[AMR][1000 genomes]
rs58063643	1.00[AMR][1000 genomes]
rs59655269	1.00[AMR][1000 genomes]
rs6033556	1.00[AMR][1000 genomes]
rs6033571	1.00[EUR][1000 genomes]
rs6033580	1.00[EUR][1000 genomes]
rs6041736	1.00[AMR][1000 genomes]
rs6041739	0.95[AFR][1000 genomes]
rs6041745	1.00[EUR][1000 genomes]
rs6041746	1.00[EUR][1000 genomes]
rs6041754	1.00[EUR][1000 genomes]
rs6041756	1.00[EUR][1000 genomes]
rs6041773	1.00[EUR][1000 genomes]
rs6041778	1.00[EUR][1000 genomes]
rs60989995	1.00[AMR][1000 genomes]
rs7271965	1.00[EUR][1000 genomes]
rs73253248	0.90[AFR][1000 genomes]
rs73265108	1.00[AMR][1000 genomes]
rs8117451	1.00[AMR][1000 genomes]
rs8124237	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	esv3431790	chr20:12940407-12948115	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12942800-12949200	Weak transcription	A549	lung
2	chr20:12945400-12948400	Enhancers	Fetal Thymus	thymus
3	chr20:12945600-12947800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:12946200-12948000	Enhancers	Fetal Brain Male	brain
5	chr20:12947400-12947800	Enhancers	Fetal Brain Female	brain
6	chr20:12947400-12949600	Enhancers	Thymus	Thymus
7	chr20:12947600-12947800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:12947600-12948600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:12947600-12949400	Weak transcription	HepG2	liver
10	chr20:12947600-12951800	Enhancers	HMEC	breast

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