Variant report

Variant	rs6050262
Chromosome Location	chr20:25015093-25015094
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	chr20:25001158..25003510-chr20:25014394..25016666,2	MCF-7	breast:
2	chr20:25014177..25016183-chr20:25020010..25021666,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12480685	1.00[EUR][1000 genomes]
rs41308619	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45509096	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050257	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050266	1.00[CEU][hapmap]
rs7263112	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24988200-25016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:24995800-25016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr20:24997200-25016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr20:24997400-25016400	Weak transcription	GM12878-XiMat	blood
5	chr20:24998600-25016600	Weak transcription	Liver	Liver
6	chr20:24999800-25016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr20:25004800-25016600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr20:25009200-25016600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr20:25010000-25017800	Weak transcription	NHDF-Ad	bronchial
10	chr20:25011200-25015200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:25011400-25016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr20:25011600-25015600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr20:25011600-25016200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr20:25011600-25016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr20:25011600-25016400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr20:25011600-25016800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr20:25011600-25017800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr20:25011600-25017800	Enhancers	Placenta	Placenta
19	chr20:25011600-25020200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr20:25011800-25016800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr20:25012000-25016400	Weak transcription	Thymus	Thymus
22	chr20:25012000-25026400	Enhancers	Right Ventricle	heart
23	chr20:25012200-25015200	Enhancers	Fetal Muscle Leg	muscle
24	chr20:25012400-25015200	Enhancers	Stomach Mucosa	stomach
25	chr20:25012400-25016400	Weak transcription	Dnd41	blood
26	chr20:25012600-25015200	Enhancers	Rectal Smooth Muscle	rectum
27	chr20:25012800-25026400	Enhancers	Brain Angular Gyrus	brain
28	chr20:25013000-25015200	Enhancers	Gastric	stomach
29	chr20:25013000-25015200	Enhancers	Pancreas	Pancrea
30	chr20:25013000-25018000	Weak transcription	Aorta	Aorta
31	chr20:25013400-25015200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr20:25013400-25015200	Enhancers	Fetal Intestine Large	intestine
33	chr20:25013400-25016400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr20:25013400-25022600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr20:25013600-25015200	Enhancers	Fetal Muscle Trunk	muscle
36	chr20:25013600-25016400	Weak transcription	Primary B cells from cord blood	blood
37	chr20:25013600-25016400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr20:25013800-25015200	Enhancers	Duodenum Mucosa	Duodenum
39	chr20:25013800-25016600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr20:25013800-25020200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr20:25014000-25016400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr20:25014000-25016800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr20:25014000-25018000	Weak transcription	Fetal Brain Female	brain
44	chr20:25014000-25018200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr20:25014000-25018200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr20:25014000-25018400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:25014000-25026400	Enhancers	Brain Cingulate Gyrus	brain
48	chr20:25014200-25016600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr20:25014200-25023000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr20:25014200-25026400	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links