Variant report

Variant	rs6036600
Chromosome Location	chr20:23979305-23979306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23918328..23919972-chr20:23977586..23980315,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGTLC1-1	chr20:23979070-23979425	XLOC_013696

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2379298	0.81[AFR][1000 genomes]
rs2379299	0.83[AFR][1000 genomes]
rs2379300	0.83[AFR][1000 genomes]
rs3843775	0.83[AFR][1000 genomes]
rs3843776	0.83[AFR][1000 genomes]
rs3843777	0.83[AFR][1000 genomes]
rs3848798	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3887942	0.86[ASN][1000 genomes]
rs4336010	0.83[AFR][1000 genomes]
rs4390824	0.83[AFR][1000 genomes]
rs4390830	0.83[AFR][1000 genomes]
rs4499504	0.83[AFR][1000 genomes]
rs4499505	0.83[AFR][1000 genomes]
rs56199073	0.83[AFR][1000 genomes]
rs57132845	0.91[ASN][1000 genomes]
rs6036606	0.83[AFR][1000 genomes]
rs6036607	0.83[AFR][1000 genomes]
rs6036609	0.83[AFR][1000 genomes]
rs6036610	0.83[AFR][1000 genomes]
rs6036611	0.83[AFR][1000 genomes]
rs6036612	0.83[AFR][1000 genomes]
rs6049299	0.99[ASN][1000 genomes]
rs6049303	0.83[AFR][1000 genomes]
rs6049305	0.83[AFR][1000 genomes]
rs6049306	0.83[AFR][1000 genomes]
rs6049307	0.83[AFR][1000 genomes]
rs6049308	0.83[AFR][1000 genomes]
rs6049309	0.83[AFR][1000 genomes]
rs6049310	0.83[AFR][1000 genomes]
rs6049311	0.83[AFR][1000 genomes]
rs6049312	0.83[AFR][1000 genomes]
rs6049313	0.83[AFR][1000 genomes]
rs6049315	0.83[AFR][1000 genomes]
rs6049316	0.83[AFR][1000 genomes]
rs6049317	0.83[AFR][1000 genomes]
rs6049319	0.83[AFR][1000 genomes]
rs6049322	0.83[AFR][1000 genomes]
rs6049323	0.83[AFR][1000 genomes]
rs6049324	0.83[AFR][1000 genomes]
rs6049325	0.83[AFR][1000 genomes]
rs6049327	0.83[AFR][1000 genomes]
rs6049328	0.84[AFR][1000 genomes]
rs6114404	0.96[ASN][1000 genomes]
rs6114406	0.97[ASN][1000 genomes]
rs9967908	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833944	chr20:23806288-24021865	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1063474	chr20:23918394-24048069	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv18738	chr20:23956042-23994680	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1806279	chr20:23956609-23980100	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23979200-23979400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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