Variant report

Variant	rs2892408
Chromosome Location	chr20:25576481-25576482
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25573368..25577137-chr20:25602924..25606486,3	MCF-7	breast:
2	chr20:25564805..25567355-chr20:25573167..25576913,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213742	Chromatin interaction
ENSG00000101004	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1569617	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16987934	0.82[ASN][1000 genomes]
rs1883528	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006249	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2103661	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2388026	0.81[AFR][1000 genomes]
rs242130	0.80[ASN][1000 genomes]
rs242133	0.98[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs35516971	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs402120	0.84[AFR][1000 genomes]
rs409322	0.84[AFR][1000 genomes]
rs4098823	0.82[AFR][1000 genomes]
rs41308623	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4280527	0.80[ASN][1000 genomes]
rs4343537	0.82[AFR][1000 genomes]
rs4813572	0.83[AFR][1000 genomes]
rs4815436	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58877578	0.94[ASN][1000 genomes]
rs6037159	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6037161	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6037164	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6037166	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6037167	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6037168	0.85[ASN][1000 genomes]
rs6037179	0.94[AFR][1000 genomes]
rs6037180	0.94[AFR][1000 genomes]
rs6037192	0.91[AFR][1000 genomes]
rs6037193	0.95[AFR][1000 genomes]
rs6037198	0.84[AFR][1000 genomes]
rs6037199	0.82[AFR][1000 genomes]
rs6037220	0.80[AFR][1000 genomes]
rs6037223	0.82[AFR][1000 genomes]
rs60394570	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6050692	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6050707	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050709	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050710	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050712	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050714	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050717	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050720	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050723	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050724	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050725	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050726	0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050727	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050729	0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050730	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050732	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050733	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050737	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050743	0.91[AFR][1000 genomes]
rs6050745	0.92[AFR][1000 genomes]
rs6050749	0.89[AFR][1000 genomes]
rs6050753	0.90[AFR][1000 genomes]
rs6050754	0.89[AFR][1000 genomes]
rs6050758	0.94[AFR][1000 genomes]
rs6050768	0.92[AFR][1000 genomes]
rs6050788	0.95[AFR][1000 genomes]
rs6050795	0.84[AFR][1000 genomes]
rs6050804	0.82[AFR][1000 genomes]
rs6050807	0.83[ASN][1000 genomes]
rs6050809	0.82[AFR][1000 genomes]
rs6050834	0.82[AFR][1000 genomes]
rs6050853	0.82[AFR][1000 genomes]
rs6076372	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083886	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6083896	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083897	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083899	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083902	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6115214	0.80[ASN][1000 genomes]
rs6115215	0.80[ASN][1000 genomes]
rs6115220	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115224	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132848	0.80[ASN][1000 genomes]
rs6132850	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138608	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138612	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138613	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7261537	0.82[ASN][1000 genomes]
rs7261902	0.94[ASN][1000 genomes]
rs7266592	0.94[ASN][1000 genomes]
rs7274550	0.94[ASN][1000 genomes]
rs73337355	0.94[ASN][1000 genomes]
rs73337356	0.94[ASN][1000 genomes]
rs73337364	0.94[ASN][1000 genomes]
rs73337366	0.94[ASN][1000 genomes]
rs73337369	0.94[ASN][1000 genomes]
rs73337372	0.94[ASN][1000 genomes]
rs73337394	0.94[ASN][1000 genomes]
rs73337401	0.94[ASN][1000 genomes]
rs73339323	0.94[ASN][1000 genomes]
rs73339335	0.94[ASN][1000 genomes]
rs73339360	0.88[ASN][1000 genomes]
rs73339379	0.82[ASN][1000 genomes]
rs73339383	0.82[ASN][1000 genomes]
rs73339387	0.82[ASN][1000 genomes]
rs73341305	0.82[ASN][1000 genomes]
rs73341314	0.82[ASN][1000 genomes]
rs73341328	0.82[ASN][1000 genomes]
rs7346687	0.90[AFR][1000 genomes]
rs8120065	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs8120594	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs8120972	0.94[ASN][1000 genomes]
rs8121013	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs8125002	0.82[ASN][1000 genomes]
rs8126111	0.88[ASN][1000 genomes]
rs8126236	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs981441	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25573800-25581000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr20:25573800-25590400	Weak transcription	Thymus	Thymus
3	chr20:25576000-25576800	Enhancers	HepG2	liver
4	chr20:25576000-25585800	Weak transcription	Fetal Stomach	stomach
5	chr20:25576400-25576600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links