Variant report

Variant	rs572553
Chromosome Location	chr4:56261018-56261019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:56260947-56266145	SK-N-SH	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56222050..56228109-chr4:56258616..56264786,10	MCF-7	breast:
2	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
3	chr4:56245537..56248832-chr4:56260791..56264132,6	MCF-7	breast:
4	chr4:56252554..56257772-chr4:56259709..56263846,8	MCF-7	breast:
5	chr4:56211096..56216124-chr4:56256262..56265067,20	K562	blood:
6	chr4:56211242..56218739-chr4:56258356..56267013,28	MCF-7	breast:
7	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
8	chr4:56260988..56264413-chr4:56410743..56414640,3	K562	blood:
9	chr4:56248184..56250642-chr4:56260280..56262635,2	K562	blood:
10	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM165	TF binding region
ENSG00000134852	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000251111	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000273257	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10010762	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10021233	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10024928	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10462028	0.85[AMR][1000 genomes]
rs17776975	0.89[ASN][1000 genomes]
rs1818460	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2538	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28609134	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3087606	1.00[ASN][1000 genomes]
rs4455482	0.95[ASN][1000 genomes]
rs475465	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476184	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs482114	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496055	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs499110	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs525271	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs550144	0.82[ASN][1000 genomes]
rs552792	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs552950	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556072	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56139168	0.89[ASN][1000 genomes]
rs572428	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573960	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs576732	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58176292	0.93[ASN][1000 genomes]
rs58506276	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59648459	0.96[ASN][1000 genomes]
rs60097207	0.89[ASN][1000 genomes]
rs62303681	0.89[ASN][1000 genomes]
rs62303685	0.82[ASN][1000 genomes]
rs62305200	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62305201	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62305202	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62305206	0.96[ASN][1000 genomes]
rs62306207	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs693367	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs819203	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs819266	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs819267	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs819268	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs819269	0.83[AMR][1000 genomes]
rs819270	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs861029	0.95[ASN][1000 genomes]
rs880358	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56248200-56261400	Weak transcription	Aorta	Aorta
3	chr4:56249200-56261200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:56252400-56261600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:56254000-56261400	Weak transcription	Fetal Thymus	thymus
6	chr4:56256000-56261200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:56256400-56261400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:56257600-56261400	Weak transcription	Pancreas	Pancrea
9	chr4:56257800-56261200	Weak transcription	Fetal Intestine Small	intestine
10	chr4:56259200-56261200	Enhancers	Brain Anterior Caudate	brain
11	chr4:56259400-56261200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:56259400-56261200	Enhancers	Brain Hippocampus Middle	brain
13	chr4:56259400-56261400	Enhancers	Brain Cingulate Gyrus	brain
14	chr4:56259400-56261600	Enhancers	Stomach Mucosa	stomach
15	chr4:56259600-56261200	Enhancers	HepG2	liver
16	chr4:56259600-56261400	Enhancers	A549	lung
17	chr4:56259800-56261200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:56259800-56261400	Weak transcription	Lung	lung
19	chr4:56260000-56261200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:56260000-56261200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:56260000-56261200	Weak transcription	NHDF-Ad	bronchial
22	chr4:56260000-56261400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:56260000-56261400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:56260000-56261600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:56260200-56261200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:56260200-56261200	Weak transcription	Brain Angular Gyrus	brain
27	chr4:56260200-56261200	Weak transcription	GM12878-XiMat	blood
28	chr4:56260200-56261200	Weak transcription	NHLF	lung
29	chr4:56260200-56261200	Weak transcription	Osteobl	bone
30	chr4:56260200-56261400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:56260200-56261400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:56260400-56261200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:56260400-56261400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:56260800-56261200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:56260800-56261400	Weak transcription	Brain Substantia Nigra	brain
36	chr4:56261000-56261200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:56261000-56261200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr4:56261000-56261200	Enhancers	Primary B cells from cord blood	blood
39	chr4:56261000-56261200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr4:56261000-56261200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:56261000-56261200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr4:56261000-56261200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:56261000-56261200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:56261000-56261200	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr4:56261000-56261200	Enhancers	HUVEC	blood vessel
46	chr4:56261000-56261200	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr4:56261000-56261400	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr4:56261000-56261400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr4:56261000-56261400	Enhancers	Dnd41	blood
50	chr4:56261000-56261400	Enhancers	HMEC	breast

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