Variant report

Variant	rs6023044
Chromosome Location	chr20:52836074-52836075
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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52835803..52837047-chr20:52936331..52937389,14	MCF-7	breast:
2	chr20:52835882..52837224-chr20:52936327..52937749,19	MCF-7	breast:
3	chr20:52835069..52840886-chr20:53069895..53074543,8	MCF-7	breast:
4	chr20:52836035..52837008-chr20:53264640..53266086,4	MCF-7	breast:
5	chr20:52834058..52838026-chr20:53082960..53086578,4	MCF-7	breast:
6	chr20:52834872..52837483-chr20:53257403..53260162,2	MCF-7	breast:
7	chr20:52830268..52836346-chr20:52932384..52936332,6	MCF-7	breast:
8	chr20:52834958..52838732-chr20:53262770..53264255,82	MCF-7	breast:
9	chr20:52834806..52836428-chr20:52863803..52865518,2	MCF-7	breast:
10	chr20:52835883..52836994-chr3:64516257..64516838,3	MCF-7	breast:
11	chr20:52835239..52838782-chr20:52890174..52893182,4	MCF-7	breast:
12	chr20:52835335..52837595-chr20:53075898..53078098,2	MCF-7	breast:
13	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
14	chr17:57919043..57920970-chr20:52833824..52836457,2	MCF-7	breast:
15	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
16	chr20:52835609..52839947-chr20:52897046..52901468,5	MCF-7	breast:
17	chr20:52835947..52837988-chr20:53095859..53097037,10	MCF-7	breast:
18	chr20:52836031..52836766-chr20:53219732..53220485,2	MCF-7	breast:
19	chr20:52835892..52837137-chr20:53264337..53265328,4	MCF-7	breast:
20	chr13:20179010..20180942-chr20:52834337..52836488,2	MCF-7	breast:
21	chr20:52834705..52836760-chr20:52964678..52966979,2	MCF-7	breast:
22	chr20:52835324..52837419-chr20:53262103..53264598,40	MCF-7	breast:
23	chr20:52823575..52825303-chr20:52835927..52837987,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11483554	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12479602	0.97[ASN][1000 genomes]
rs12624322	0.95[ASN][1000 genomes]
rs12624646	0.91[ASN][1000 genomes]
rs12625916	0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs1418926	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1418927	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs1961795	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6091836	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6097867	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6127138	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs62216577	1.00[ASN][1000 genomes]
rs62216585	0.87[ASN][1000 genomes]
rs7267971	0.82[ASN][1000 genomes]
rs7270114	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73137408	1.00[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6023044	ENSG00000101132	cis	multi-tissue	Pritchard
rs6023044	AURKA	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52825400-52838800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:52825600-52839000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:52826000-52837200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:52826000-52837800	Weak transcription	Fetal Thymus	thymus
5	chr20:52826000-52838200	Weak transcription	Pancreas	Pancrea
6	chr20:52826000-52840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:52826200-52838800	Weak transcription	Gastric	stomach
8	chr20:52826600-52836800	Weak transcription	Liver	Liver
9	chr20:52826600-52837400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr20:52826600-52838200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr20:52826600-52838800	Weak transcription	Brain Anterior Caudate	brain
12	chr20:52826800-52837200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr20:52826800-52838200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr20:52826800-52838400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:52826800-52838800	Weak transcription	Brain Hippocampus Middle	brain
16	chr20:52827000-52836200	Weak transcription	Small Intestine	intestine
17	chr20:52827000-52838400	Weak transcription	Fetal Brain Male	brain
18	chr20:52827000-52838800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr20:52827000-52838800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr20:52827000-52838800	Weak transcription	Fetal Lung	lung
21	chr20:52827000-52838800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr20:52827200-52838800	Weak transcription	Right Atrium	heart
23	chr20:52827200-52841000	Weak transcription	Brain Germinal Matrix	brain
24	chr20:52829200-52837800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr20:52829400-52847400	Weak transcription	Aorta	Aorta
26	chr20:52829600-52838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr20:52829600-52838800	Weak transcription	NH-A	brain
28	chr20:52829600-52847600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr20:52829800-52836600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr20:52829800-52837800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr20:52830000-52838800	Weak transcription	NHDF-Ad	bronchial
32	chr20:52830000-52839200	Weak transcription	Ovary	ovary
33	chr20:52830200-52836800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr20:52830600-52837000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr20:52830800-52837400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr20:52831200-52836600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr20:52831200-52836600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr20:52831400-52842200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr20:52832200-52838600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr20:52832600-52837800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr20:52832600-52838000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr20:52832800-52838600	Weak transcription	HMEC	breast
43	chr20:52833000-52838200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr20:52833000-52838200	Weak transcription	Fetal Kidney	kidney
45	chr20:52833000-52838600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr20:52833000-52845400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:52834000-52836600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr20:52834000-52838200	Weak transcription	Esophagus	oesophagus
49	chr20:52834000-52838800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr20:52834000-52838800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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