Variant report

Variant	rs60394570
Chromosome Location	chr20:25584003-25584004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25581473..25584276-chr20:25603857..25605738,2	K562	blood:
2	chr20:25581299..25586315-chr20:25601577..25606333,5	MCF-7	breast:
3	chr20:25582607..25585301-chr20:25602976..25605414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170191	Chromatin interaction
ENSG00000213742	Chromatin interaction

Extended variants
information (count: 160 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1569617	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16987934	0.83[ASN][1000 genomes]
rs1883528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2006249	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2103661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2388026	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs242130	0.81[ASN][1000 genomes]
rs242133	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2892408	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35516971	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3764695	0.80[ASN][1000 genomes]
rs402120	0.82[AFR][1000 genomes]
rs409322	0.82[AFR][1000 genomes]
rs4098823	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4098824	0.80[ASN][1000 genomes]
rs4113658	0.80[ASN][1000 genomes]
rs4113659	0.80[ASN][1000 genomes]
rs4113662	0.80[ASN][1000 genomes]
rs41308623	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4343537	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4574179	0.80[ASN][1000 genomes]
rs4813572	0.81[AFR][1000 genomes]
rs4815436	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57638633	0.80[ASN][1000 genomes]
rs58877578	0.83[ASN][1000 genomes]
rs6037159	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6037161	0.95[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6037164	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6037166	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6037167	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6037168	0.86[ASN][1000 genomes]
rs6037179	0.95[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6037180	0.95[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6037192	0.90[AFR][1000 genomes]
rs6037193	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6037198	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6037199	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6037208	0.80[ASN][1000 genomes]
rs6037212	0.80[ASN][1000 genomes]
rs6037217	0.80[ASN][1000 genomes]
rs6037220	0.80[ASN][1000 genomes]
rs6037223	0.81[AFR][1000 genomes]
rs6050692	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050707	0.97[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050709	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050710	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050712	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050714	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050717	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050720	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050723	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050724	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050725	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050726	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050727	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050729	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050730	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050732	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050733	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050737	0.95[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6050743	0.91[AFR][1000 genomes]
rs6050745	0.92[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050749	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050753	0.92[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050754	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050755	0.80[ASN][1000 genomes]
rs6050756	0.80[ASN][1000 genomes]
rs6050758	0.95[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050765	0.80[ASN][1000 genomes]
rs6050768	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050775	0.80[ASN][1000 genomes]
rs6050787	0.80[ASN][1000 genomes]
rs6050788	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050789	0.80[ASN][1000 genomes]
rs6050795	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050799	0.80[ASN][1000 genomes]
rs6050802	0.80[ASN][1000 genomes]
rs6050804	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050807	0.83[ASN][1000 genomes]
rs6050809	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050832	0.80[ASN][1000 genomes]
rs6050834	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050835	0.80[ASN][1000 genomes]
rs6050838	0.80[ASN][1000 genomes]
rs6050841	0.80[ASN][1000 genomes]
rs6050846	0.80[ASN][1000 genomes]
rs6050847	0.80[ASN][1000 genomes]
rs6050848	0.80[ASN][1000 genomes]
rs6050851	0.80[ASN][1000 genomes]
rs6050853	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6050854	0.80[ASN][1000 genomes]
rs6076372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083886	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6083896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083897	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083902	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6115220	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6115224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132850	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138608	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138612	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138613	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7261537	0.83[ASN][1000 genomes]
rs7261902	0.83[ASN][1000 genomes]
rs7266592	0.83[ASN][1000 genomes]
rs7274550	0.83[ASN][1000 genomes]
rs73337355	0.83[ASN][1000 genomes]
rs73337356	0.83[ASN][1000 genomes]
rs73337364	0.83[ASN][1000 genomes]
rs73337366	0.83[ASN][1000 genomes]
rs73337369	0.83[ASN][1000 genomes]
rs73337372	0.83[ASN][1000 genomes]
rs73337394	0.83[ASN][1000 genomes]
rs73337401	0.83[ASN][1000 genomes]
rs73339323	0.83[ASN][1000 genomes]
rs73339335	0.83[ASN][1000 genomes]
rs73339360	0.89[ASN][1000 genomes]
rs73339379	0.83[ASN][1000 genomes]
rs73339383	0.83[ASN][1000 genomes]
rs73339387	0.83[ASN][1000 genomes]
rs73341305	0.83[ASN][1000 genomes]
rs73341314	0.83[ASN][1000 genomes]
rs73341328	0.83[ASN][1000 genomes]
rs73341361	0.80[ASN][1000 genomes]
rs73341397	0.80[ASN][1000 genomes]
rs73343217	0.80[ASN][1000 genomes]
rs73343255	0.80[ASN][1000 genomes]
rs73345232	0.80[ASN][1000 genomes]
rs7346687	0.92[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs8120065	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8120594	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8120972	0.83[ASN][1000 genomes]
rs8121013	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8125002	0.83[ASN][1000 genomes]
rs8126236	0.95[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs926487	0.80[ASN][1000 genomes]
rs9753575	0.80[ASN][1000 genomes]
rs981440	0.80[ASN][1000 genomes]
rs981441	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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
17	esv3403907	chr20:25581152-25585550	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	esv3420631	chr20:25581977-25584725	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv3515002	chr20:25582377-25584600	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv3515003	chr20:25582377-25584600	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25573800-25590400	Weak transcription	Thymus	Thymus
2	chr20:25576000-25585800	Weak transcription	Fetal Stomach	stomach
3	chr20:25580200-25603000	Weak transcription	Fetal Brain Male	brain
4	chr20:25581600-25594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr20:25581800-25594000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:25581800-25603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:25582000-25593200	Weak transcription	Adipose Nuclei	Adipose
8	chr20:25582000-25594800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:25582000-25602800	Weak transcription	Osteobl	bone
10	chr20:25582200-25585200	Weak transcription	HSMMtube	muscle
11	chr20:25582200-25593000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr20:25583600-25594200	Weak transcription	Aorta	Aorta
13	chr20:25583800-25584200	Flanking Active TSS	HepG2	liver
14	chr20:25583800-25584400	Enhancers	Liver	Liver
15	chr20:25584000-25588400	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links