Variant report

Variant	rs12480685
Chromosome Location	chr20:25002763-25002764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24998233..25001410-chr20:25002125..25005699,3	MCF-7	breast:
2	chr20:25001474..25003157-chr20:25012221..25014291,2	MCF-7	breast:
3	chr20:25001158..25003510-chr20:25014394..25016666,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs41308619	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45509096	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050257	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050262	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24981600-25003600	Weak transcription	Fetal Heart	heart
2	chr20:24983200-25003800	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr20:24983200-25005000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr20:24983200-25007800	Strong transcription	Primary T cells from cord blood	blood
5	chr20:24983200-25008200	Strong transcription	Primary B cells from cord blood	blood
6	chr20:24983800-25006800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr20:24985000-25004400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr20:24985000-25005600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr20:24985200-25003200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr20:24985200-25007800	Strong transcription	Fetal Muscle Leg	muscle
11	chr20:24985800-25004200	Strong transcription	Thymus	Thymus
12	chr20:24985800-25004400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr20:24985800-25005000	Strong transcription	Adipose Nuclei	Adipose
14	chr20:24985800-25005800	Strong transcription	Spleen	Spleen
15	chr20:24985800-25006800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:24985800-25007600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr20:24985800-25007800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr20:24986000-25004800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr20:24986200-25012400	Strong transcription	Dnd41	blood
20	chr20:24986400-25003800	Strong transcription	Aorta	Aorta
21	chr20:24986400-25004400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr20:24986400-25012400	Weak transcription	Fetal Brain Male	brain
23	chr20:24987400-25005200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr20:24987600-25007800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr20:24988200-25016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr20:24991000-25002800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr20:24993400-25005200	Weak transcription	Psoas Muscle	Psoas
28	chr20:24993800-25013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr20:24994000-25013000	Weak transcription	Small Intestine	intestine
30	chr20:24994800-25006800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr20:24994800-25013200	Weak transcription	Fetal Brain Female	brain
32	chr20:24995800-25016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr20:24996200-25010200	Weak transcription	Colon Smooth Muscle	Colon
34	chr20:24996600-25005200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr20:24996600-25007800	Genic enhancers	Placenta	Placenta
36	chr20:24997200-25007400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr20:24997200-25016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr20:24997400-25007800	Strong transcription	Fetal Stomach	stomach
39	chr20:24997400-25016400	Weak transcription	GM12878-XiMat	blood
40	chr20:24998600-25011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr20:24998600-25016600	Weak transcription	Liver	Liver
42	chr20:24998800-25003000	Weak transcription	NHEK	skin
43	chr20:24998800-25003200	Strong transcription	Fetal Intestine Small	intestine
44	chr20:24998800-25010200	Weak transcription	Fetal Lung	lung
45	chr20:24999000-25003200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr20:24999000-25003200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr20:24999600-25003000	Strong transcription	Fetal Intestine Large	intestine
48	chr20:24999800-25004200	Weak transcription	Fetal Thymus	thymus
49	chr20:24999800-25005000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr20:24999800-25016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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