Variant report

Variant	rs56378040
Chromosome Location	chr20:52507510-52507511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52502125..52504611-chr20:52505753..52508666,2	K562	blood:
2	chr20:52502125..52504163-chr20:52505753..52508684,2	K562	blood:
3	chr20:52507107..52509480-chr8:90914201..90916208,2	MCF-7	breast:
4	chr20:52507216..52510163-chr20:55822269..55824456,2	MCF-7	breast:
5	chr17:61524420..61527001-chr20:52506078..52507806,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs7260830	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73912533	1.00[AMR][1000 genomes]
rs73914416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
5	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52500600-52515600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:52501800-52508400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:52501800-52509200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr20:52501800-52509400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr20:52501800-52509400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:52501800-52509400	Weak transcription	Thymus	Thymus
7	chr20:52501800-52509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr20:52502000-52509400	Weak transcription	Primary T cells from cord blood	blood
9	chr20:52502200-52509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr20:52502200-52509600	Weak transcription	NHEK	skin
11	chr20:52502600-52509400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr20:52502800-52509400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr20:52503000-52509400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr20:52503800-52509400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr20:52505400-52508800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr20:52505400-52509400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr20:52505400-52509400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr20:52505600-52508000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr20:52505600-52508400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr20:52505800-52508400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr20:52505800-52508600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr20:52505800-52509400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr20:52505800-52509400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr20:52505800-52509400	Weak transcription	Fetal Thymus	thymus
25	chr20:52506400-52508000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:52506800-52509800	Enhancers	NHLF	lung
27	chr20:52507000-52507600	Enhancers	Osteobl	bone
28	chr20:52507000-52507800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr20:52507000-52507800	Enhancers	Fetal Intestine Large	intestine
30	chr20:52507000-52507800	Enhancers	Placenta	Placenta
31	chr20:52507000-52507800	Enhancers	Small Intestine	intestine
32	chr20:52507000-52507800	Enhancers	Spleen	Spleen
33	chr20:52507000-52508000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr20:52507000-52508200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr20:52507000-52508200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr20:52507000-52508200	Enhancers	Duodenum Mucosa	Duodenum
37	chr20:52507000-52508200	Enhancers	Fetal Intestine Small	intestine
38	chr20:52507000-52508400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr20:52507000-52508600	Enhancers	HUVEC	blood vessel
40	chr20:52507000-52508800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr20:52507000-52509000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr20:52507200-52507600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr20:52507200-52507800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr20:52507200-52508000	Enhancers	A549	lung
45	chr20:52507200-52510400	Enhancers	NH-A	brain
46	chr20:52507400-52507600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr20:52507400-52507600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr20:52507400-52507600	Weak transcription	Adipose Nuclei	Adipose
49	chr20:52507400-52507800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr20:52507400-52508000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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