Variant report

Variant	rs292112
Chromosome Location	chr20:52839146-52839147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52838977..52840544-chr20:52845330..52847377,2	K562	blood:
2	chr20:52838765..52840477-chr20:52844593..52846830,2	K562	blood:
3	chr20:52835069..52840886-chr20:53069895..53074543,8	MCF-7	breast:
4	chr20:52838097..52840122-chr20:52937035..52938814,2	MCF-7	breast:
5	chr20:52390713..52393144-chr20:52838383..52839973,2	MCF-7	breast:
6	chr20:52837790..52839838-chr20:53004656..53006730,2	MCF-7	breast:
7	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
8	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
9	chr20:52835609..52839947-chr20:52897046..52901468,5	MCF-7	breast:
10	chr20:45988897..45990443-chr20:52838117..52840797,2	MCF-7	breast:
11	chr1:228537810..228540414-chr20:52836573..52839154,2	MCF-7	breast:
12	chr20:52837337..52840650-chr20:52960350..52963395,3	MCF-7	breast:
13	chr20:52838984..52839649-chr20:53263391..53263996,2	MCF-7	breast:
14	chr20:52838493..52841252-chr20:52870452..52872363,2	MCF-7	breast:
15	chr20:52838614..52841427-chr20:52933611..52935858,2	MCF-7	breast:
16	chr20:52836430..52839312-chr20:53251846..53253963,2	MCF-7	breast:
17	chr20:52837175..52839951-chr20:52903324..52905854,2	MCF-7	breast:
18	chr20:52836483..52840611-chr20:52882316..52886295,8	MCF-7	breast:

No data

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11698157	0.96[ASN][1000 genomes]
rs1382007	0.88[ASN][1000 genomes]
rs292116	0.92[JPT][hapmap]
rs292117	0.92[JPT][hapmap]
rs3787559	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs56726174	0.89[EUR][1000 genomes]
rs6013926	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6013927	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6013930	0.83[TSI][hapmap]
rs6023079	0.84[JPT][hapmap]
rs6097840	0.83[TSI][hapmap]
rs6127146	0.93[ASN][1000 genomes]
rs73137406	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs986709	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 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	chr20:52826000-52840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:52827200-52841000	Weak transcription	Brain Germinal Matrix	brain
3	chr20:52829400-52847400	Weak transcription	Aorta	Aorta
4	chr20:52829600-52847600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr20:52830000-52839200	Weak transcription	Ovary	ovary
6	chr20:52831400-52842200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr20:52833000-52845400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr20:52834200-52840800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr20:52834200-52841000	Weak transcription	Primary B cells from cord blood	blood
10	chr20:52834200-52841200	Weak transcription	Spleen	Spleen
11	chr20:52834200-52843600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr20:52834600-52840000	Weak transcription	Psoas Muscle	Psoas
13	chr20:52834600-52840600	Weak transcription	Lung	lung
14	chr20:52834600-52840600	Weak transcription	Thymus	Thymus
15	chr20:52834600-52843600	Weak transcription	GM12878-XiMat	blood
16	chr20:52834600-52845200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:52834600-52845200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr20:52834600-52845200	Weak transcription	NHEK	skin
19	chr20:52835600-52845800	Weak transcription	HSMM	muscle
20	chr20:52835600-52846000	Weak transcription	HSMMtube	muscle
21	chr20:52835800-52839200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr20:52836800-52839200	Strong transcription	HepG2	liver
23	chr20:52836800-52839400	Strong transcription	Fetal Stomach	stomach
24	chr20:52837200-52839400	Enhancers	Fetal Brain Female	brain
25	chr20:52837200-52840800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr20:52837400-52839400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr20:52837400-52839400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr20:52837400-52839400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr20:52837400-52839800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr20:52837400-52842200	Weak transcription	Dnd41	blood
31	chr20:52837600-52839400	Enhancers	Adipose Nuclei	Adipose
32	chr20:52837600-52841000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr20:52837800-52839200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr20:52837800-52839200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr20:52837800-52839200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr20:52837800-52839200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr20:52837800-52839200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr20:52837800-52839200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr20:52837800-52839400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr20:52837800-52839400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr20:52837800-52839400	Enhancers	Fetal Thymus	thymus
42	chr20:52837800-52840800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr20:52837800-52841000	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr20:52838000-52839200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr20:52838000-52839200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr20:52838000-52839400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr20:52838000-52839600	Weak transcription	Fetal Intestine Small	intestine
48	chr20:52838000-52841000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr20:52838200-52839200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr20:52838200-52839200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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