Variant report

Variant	rs12624679
Chromosome Location	chr20:25070943-25070944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25064909..25066884-chr20:25069221..25071356,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VSX1-3	chr20:25069434-25071467	l_2095_NR_027093
2	lnc-VSX1-3	chr20:25069425-25071467	NONHSAT079125

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6138482	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66817095	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 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	chr20:25068200-25071000	Enhancers	Fetal Thymus	thymus
2	chr20:25069800-25071400	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr20:25069800-25073200	Flanking Active TSS	Dnd41	blood
4	chr20:25070000-25071000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr20:25070000-25071200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr20:25070000-25073400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr20:25070000-25073600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr20:25070400-25071000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr20:25070400-25071400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr20:25070400-25072800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr20:25070400-25073000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr20:25070400-25073200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr20:25070400-25073200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr20:25070600-25071200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr20:25070600-25071400	Enhancers	Primary T cells from cord blood	blood
16	chr20:25070600-25071400	Flanking Active TSS	Thymus	Thymus
17	chr20:25070600-25073000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr20:25070600-25073400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr20:25070800-25072200	Enhancers	Duodenum Mucosa	Duodenum
20	chr20:25070800-25073000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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