Variant report

Variant	rs60531117
Chromosome Location	chr20:24762592-24762593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24283824..24284530-chr20:24761681..24762698,3	MCF-7	breast:
2	chr20:24082874..24083567-chr20:24762073..24762659,2	MCF-7	breast:
3	chr20:24283757..24284263-chr20:24761732..24762710,2	MCF-7	breast:
4	chr20:24760897..24762927-chr20:24971923..24974297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs55760035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58684827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59252648	1.00[AMR][1000 genomes]
rs59901088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61350955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7270151	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7272053	0.81[AMR][1000 genomes]
rs7272507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7274081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903587	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903916	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903922	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903930	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903931	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903935	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903938	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73903969	0.90[AMR][1000 genomes]
rs73903971	0.90[AMR][1000 genomes]
rs73903972	0.90[AMR][1000 genomes]
rs73903974	0.90[AMR][1000 genomes]
rs73903977	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061281	chr20:24711635-24815107	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv544217	chr20:24711635-24815107	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv912825	chr20:24715544-24813345	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1061455	chr20:24733120-24861801	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv544218	chr20:24733120-24861801	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1059270	chr20:24741923-24787243	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24749200-24763600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:24757800-24766600	Enhancers	Fetal Thymus	thymus
3	chr20:24758400-24766800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr20:24758600-24763800	Enhancers	Fetal Muscle Leg	muscle
5	chr20:24758800-24767400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr20:24759800-24767000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr20:24761000-24762800	Enhancers	Stomach Smooth Muscle	stomach
8	chr20:24761200-24763400	Enhancers	Brain Substantia Nigra	brain
9	chr20:24761400-24764000	Enhancers	Brain Hippocampus Middle	brain
10	chr20:24761400-24765200	Weak transcription	Primary T cells from cord blood	blood
11	chr20:24761800-24762800	Enhancers	Brain Anterior Caudate	brain
12	chr20:24762000-24762600	Weak transcription	Fetal Lung	lung
13	chr20:24762200-24763400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:24762200-24767000	Enhancers	Dnd41	blood
15	chr20:24762400-24762600	Enhancers	Colon Smooth Muscle	Colon
16	chr20:24762400-24762800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr20:24762400-24762800	Weak transcription	Thymus	Thymus
18	chr20:24762400-24763400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:24762400-24763600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr20:24762400-24765400	Weak transcription	GM12878-XiMat	blood

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