Variant report

Variant	rs1055251
Chromosome Location	chr20:52560784-52560785
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:43)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:43 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52559353..52561066-chr20:52815864..52817031,20	MCF-7	breast:
2	chr17:62398103..62399042-chr20:52560051..52560948,3	MCF-7	breast:
3	chr20:52368008..52370445-chr20:52559869..52562207,2	K562	blood:
4	chr17:59474996..59480161-chr20:52556121..52561884,6	MCF-7	breast:
5	chr20:52560038..52560811-chr3:64016040..64016615,3	MCF-7	breast:
6	chr20:52559941..52560798-chr20:55827379..55828354,3	MCF-7	breast:
7	chr20:52560304..52562724-chr20:52567019..52568776,2	K562	blood:
8	chr17:62398176..62399003-chr20:52560040..52560894,2	MCF-7	breast:
9	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
10	chr20:52560480..52562741-chr20:55768804..55771635,2	MCF-7	breast:
11	chr17:59938922..59941556-chr20:52559570..52562678,4	MCF-7	breast:
12	chr20:52559962..52561071-chr20:55755658..55756633,7	MCF-7	breast:
13	chr20:52559752..52562075-chr20:52740413..52742422,2	MCF-7	breast:
14	chr20:52557746..52563146-chr20:52657006..52659772,4	MCF-7	breast:
15	chr20:52531990..52532987-chr20:52560322..52560880,3	MCF-7	breast:
16	chr20:52560024..52560977-chr20:52673636..52674212,3	MCF-7	breast:
17	chr20:52559543..52560922-chr20:52815975..52816881,12	MCF-7	breast:
18	chr17:59713191..59714015-chr20:52559927..52560791,5	MCF-7	breast:
19	chr20:52559967..52560815-chr3:64015981..64016917,4	MCF-7	breast:
20	chr20:52195014..52196203-chr20:52559962..52560949,9	MCF-7	breast:
21	chr20:52559479..52560840-chr20:53297067..53298188,6	MCF-7	breast:
22	chr20:52559960..52560793-chr20:55755765..55756269,2	MCF-7	breast:
23	chr17:65105910..65108534-chr20:52559281..52562207,2	MCF-7	breast:
24	chr20:52560140..52560953-chr20:55840787..55841663,3	MCF-7	breast:
25	chr20:52559928..52560938-chr20:55798386..55799365,4	MCF-7	breast:
26	chr20:52558981..52564129-chr20:55836783..55844481,11	MCF-7	breast:
27	chr20:52560251..52560815-chr3:107477140..107477823,2	MCF-7	breast:
28	chr17:59493945..59494456-chr20:52560394..52560907,2	MCF-7	breast:
29	chr20:52559798..52560894-chr20:52814273..52815363,3	MCF-7	breast:
30	chr20:52559629..52560938-chr20:52573970..52574859,6	MCF-7	breast:
31	chr20:52559216..52560998-chr20:52678738..52679912,14	MCF-7	breast:
32	chr20:52559894..52560944-chr20:55819143..55820346,5	MCF-7	breast:
33	chr19:36979934..36982567-chr20:52560633..52562262,2	MCF-7	breast:
34	chr20:52559378..52561018-chr20:52678965..52680200,31	MCF-7	breast:
35	chr20:52559935..52560798-chr20:52712964..52713952,4	MCF-7	breast:
36	chr20:52560027..52561332-chr20:52573988..52574832,5	MCF-7	breast:
37	chr20:52531996..52533073-chr20:52559900..52560972,7	MCF-7	breast:
38	chr20:52560199..52561160-chr20:52568299..52569413,3	MCF-7	breast:
39	chr20:46426563..46428367-chr20:52559861..52561851,2	MCF-7	breast:
40	chr20:52195051..52196095-chr20:52559555..52561243,28	MCF-7	breast:
41	chr20:52560012..52562267-chr20:55711106..55712686,2	MCF-7	breast:
42	chr20:52559436..52563204-chr20:52814345..52818014,8	MCF-7	breast:
43	chr20:52560247..52562300-chr20:55803016..55805479,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267309	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000186017	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1055249	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141264	0.82[AMR][1000 genomes]
rs6013844	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6013845	0.82[TSI][hapmap]
rs6022863	0.81[CEU][hapmap]
rs6022865	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6123329	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs719204	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732377	0.83[LWK][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	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	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
3	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
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv820262	chr20:52560768-52561389	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1055251	ATP9A	cis	cerebellum	SCAN
rs1055251	FAM65C	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr20:52552200-52565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:52552600-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr20:52554600-52561000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr20:52554800-52565000	Weak transcription	Spleen	Spleen
7	chr20:52555400-52561000	Enhancers	Fetal Heart	heart
8	chr20:52556400-52560800	Enhancers	Primary B cells from cord blood	blood
9	chr20:52556400-52561000	Enhancers	Fetal Lung	lung
10	chr20:52556400-52564000	Weak transcription	Esophagus	oesophagus
11	chr20:52556400-52564000	Weak transcription	Gastric	stomach
12	chr20:52556400-52565400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr20:52556600-52566000	Weak transcription	Aorta	Aorta
14	chr20:52556800-52564000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr20:52557000-52564200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr20:52557200-52565000	Weak transcription	Left Ventricle	heart
17	chr20:52557400-52569200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr20:52557800-52560800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr20:52557800-52560800	Enhancers	Fetal Brain Female	brain
20	chr20:52557800-52560800	Enhancers	HSMM	muscle
21	chr20:52557800-52561000	Enhancers	Fetal Brain Male	brain
22	chr20:52557800-52565400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr20:52558000-52560800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr20:52558000-52560800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr20:52558000-52560800	Enhancers	Brain Cingulate Gyrus	brain
26	chr20:52558000-52560800	Enhancers	Brain Hippocampus Middle	brain
27	chr20:52558000-52560800	Enhancers	Brain Substantia Nigra	brain
28	chr20:52558000-52561000	Enhancers	Primary B cells from peripheral blood	blood
29	chr20:52558000-52561000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr20:52558000-52561000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr20:52558000-52565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr20:52558000-52565400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr20:52558000-52565400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr20:52558000-52565800	Weak transcription	Colonic Mucosa	Colon
35	chr20:52558000-52566000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr20:52558400-52561000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr20:52558400-52561000	Enhancers	Brain Anterior Caudate	brain
38	chr20:52558400-52569000	Weak transcription	Fetal Intestine Small	intestine
39	chr20:52558600-52561000	Enhancers	Stomach Mucosa	stomach
40	chr20:52558800-52564200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr20:52558800-52565200	Weak transcription	Small Intestine	intestine
42	chr20:52559000-52560800	Enhancers	HepG2	liver
43	chr20:52559000-52561200	Weak transcription	HSMMtube	muscle
44	chr20:52559000-52565400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr20:52559200-52560800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr20:52559200-52560800	Enhancers	Liver	Liver
47	chr20:52559200-52565400	Weak transcription	Right Atrium	heart
48	chr20:52559400-52560800	Enhancers	GM12878-XiMat	blood
49	chr20:52559400-52565000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr20:52559400-52565000	Weak transcription	Rectal Mucosa Donor 29	rectum

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