Variant report

Variant	rs58820431
Chromosome Location	chr12:120976244-120976245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr12:120975520-120977758	IMR90	lung:	n/a	n/a
2	RXRA	chr12:120976170-120976943	SK-N-SH	brain:	n/a	chr12:120976559-120976575
3	NFIC	chr12:120976194-120976973	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr12:120976244-120977624	SK-N-SH	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120975914..120977985-chr12:120980221..120984340,3	K562	blood:
2	chr12:120934821..120937142-chr12:120975702..120977289,2	K562	blood:
3	chr12:120904864..120906819-chr12:120975505..120978250,2	K562	blood:
4	chr12:120974713..120977550-chr12:122230607..122232618,2	MCF-7	breast:
5	chr12:120932415..120934356-chr12:120975182..120977276,3	K562	blood:
6	chr12:120974437..120977304-chr12:120987855..120989624,2	K562	blood:
7	chr12:120729040..120730997-chr12:120974004..120976288,2	MCF-7	breast:
8	chr12:120971037..120975304-chr12:120975944..120978550,4	MCF-7	breast:
9	chr12:120974815..120979080-chr12:120980221..120984438,7	K562	blood:
10	chr12:120932415..120935413-chr12:120975182..120978134,3	K562	blood:
11	chr12:120965752..120968769-chr12:120974337..120978260,3	MCF-7	breast:

No data

Variant related genes	Relation type
COQ5	TF binding region
ENSG00000248008	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000110871	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000088986	Chromatin interaction
ENSG00000022840	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10515974	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1167257	1.00[EUR][1000 genomes]
rs13343210	1.00[EUR][1000 genomes]
rs16950279	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16950282	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1794740	1.00[EUR][1000 genomes]
rs2233672	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2522132	1.00[EUR][1000 genomes]
rs56821784	0.85[AMR][1000 genomes]
rs57810519	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58440772	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58811988	1.00[EUR][1000 genomes]
rs59046982	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59055537	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59211409	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59253114	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59349654	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59986216	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60688174	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6490298	1.00[EUR][1000 genomes]
rs7304206	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906	chr12:120973683-121018441	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120972800-120977400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:120972800-120977600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:120973000-120977200	Flanking Active TSS	Rectal Smooth Muscle	rectum
4	chr12:120973000-120977400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:120973000-120980200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:120973200-120977000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr12:120973200-120977000	Flanking Active TSS	Brain Angular Gyrus	brain
8	chr12:120973200-120977400	Flanking Active TSS	HUVEC	blood vessel
9	chr12:120973400-120976800	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr12:120973400-120984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:120973600-120976400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr12:120973600-120976600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:120973800-120984000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:120974000-120976600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:120974000-120977200	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr12:120974000-120977800	Enhancers	Spleen	Spleen
17	chr12:120974200-120976800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:120974200-120976800	Flanking Active TSS	HepG2	liver
19	chr12:120974200-120978600	Genic enhancers	Fetal Muscle Leg	muscle
20	chr12:120974400-120976600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:120974400-120976600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:120974400-120977400	Genic enhancers	Fetal Thymus	thymus
23	chr12:120974400-120977600	Enhancers	Stomach Mucosa	stomach
24	chr12:120974400-120977600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr12:120974400-120984200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:120974600-120976600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:120974600-120976600	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr12:120974600-120976800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:120974600-120976800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr12:120974600-120977400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:120974600-120977400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:120974600-120978600	Genic enhancers	Fetal Intestine Small	intestine
33	chr12:120974600-120979000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:120974600-120979400	Genic enhancers	K562	blood
35	chr12:120974600-120984000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:120974800-120976400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr12:120974800-120976600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:120974800-120977000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
39	chr12:120974800-120977400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:120974800-120977400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr12:120974800-120977400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr12:120974800-120978200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr12:120975000-120976400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:120975000-120976400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:120975000-120977400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr12:120975200-120976400	Weak transcription	Esophagus	oesophagus
47	chr12:120975200-120976800	Genic enhancers	Thymus	Thymus
48	chr12:120975200-120980000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:120975200-120982400	Enhancers	Pancreas	Pancrea
50	chr12:120975200-120985200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links