Variant report

Variant	rs28507080
Chromosome Location	chr4:56828880-56828881
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56814955..56816833-chr4:56828456..56830124,2	K562	blood:
2	chr4:56820475..56822078-chr4:56827472..56830252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174799	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10033331	0.81[ASN][1000 genomes]
rs10212814	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10517365	0.84[ASN][1000 genomes]
rs10866430	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11133419	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11724411	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11726419	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731842	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11732545	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734217	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11933720	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11934142	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11937929	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945709	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12642567	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12645491	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13112832	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13121634	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13127483	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13129197	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17797425	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2290014	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472524	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28610174	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3214045	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34285861	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35003282	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35123416	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35814086	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3806749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4499751	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59511278	0.86[ASN][1000 genomes]
rs62308565	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62308614	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62308617	0.86[ASN][1000 genomes]
rs62308621	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6814923	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6815354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823178	0.86[ASN][1000 genomes]
rs6830668	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6849999	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670026	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56815800-56839200	Weak transcription	Esophagus	oesophagus
2	chr4:56815800-56875000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:56816000-56833400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:56816200-56839400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:56816200-56846600	Weak transcription	Right Ventricle	heart
6	chr4:56816200-56873400	Weak transcription	Pancreas	Pancrea
7	chr4:56816200-56884200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:56816200-56887800	Weak transcription	Gastric	stomach
9	chr4:56816400-56866000	Weak transcription	Spleen	Spleen
10	chr4:56816400-56890800	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:56816600-56829800	Weak transcription	Colonic Mucosa	Colon
12	chr4:56816600-56831800	Weak transcription	Fetal Lung	lung
13	chr4:56816600-56834000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:56816600-56851800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:56816600-56852000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:56816600-56865800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:56816600-56890600	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:56816600-56896400	Weak transcription	Fetal Heart	heart
19	chr4:56816800-56831400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:56816800-56865800	Weak transcription	Small Intestine	intestine
21	chr4:56816800-56869800	Weak transcription	HepG2	liver
22	chr4:56817400-56839200	Weak transcription	NHEK	skin
23	chr4:56817400-56885400	Weak transcription	NHDF-Ad	bronchial
24	chr4:56817800-56846200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:56817800-56854600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:56818200-56837200	Strong transcription	Fetal Thymus	thymus
27	chr4:56818200-56853800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:56818400-56829800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:56818400-56831000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:56818400-56833000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr4:56818800-56841800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:56819000-56835400	Strong transcription	Dnd41	blood
33	chr4:56819000-56897400	Weak transcription	HSMMtube	muscle
34	chr4:56819200-56859600	Weak transcription	Fetal Kidney	kidney
35	chr4:56819200-56890600	Weak transcription	NHLF	lung
36	chr4:56820000-56841600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:56820400-56829600	Strong transcription	Primary T cells from cord blood	blood
38	chr4:56820600-56829000	Weak transcription	HSMM	muscle
39	chr4:56820600-56892400	Weak transcription	Hela-S3	cervix
40	chr4:56821600-56831400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:56822200-56849800	Weak transcription	Fetal Brain Male	brain
42	chr4:56822200-56873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr4:56822400-56829000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:56822400-56845000	Weak transcription	K562	blood
45	chr4:56822400-56865800	Weak transcription	Psoas Muscle	Psoas
46	chr4:56822800-56829000	Weak transcription	Osteobl	bone
47	chr4:56823600-56893800	Weak transcription	HMEC	breast
48	chr4:56824000-56846600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:56824200-56829000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:56824200-56829000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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