Variant report

Variant	rs28453686
Chromosome Location	chr2:172307474-172307475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr2:172307454-172308086	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:172307469-172307706	K562	blood:	n/a	n/a
3	EP300	chr2:172307350-172308037	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr2:172307395-172308266	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr2:172307471-172308117	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:172307434-172308241	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172297612..172303267-chr2:172305217..172308512,5	K562	blood:
2	chr2:172289123..172294777-chr2:172305458..172308924,10	K562	blood:
3	chr2:172289123..172292836-chr2:172306272..172310763,6	K562	blood:

Variant related genes	Relation type
DCAF17	TF binding region
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs57136707	0.95[AFR][1000 genomes]
rs59019079	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59195571	0.85[AFR][1000 genomes]
rs59827170	0.83[AFR][1000 genomes]
rs60601337	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6729749	0.95[AFR][1000 genomes]
rs6730160	0.95[AFR][1000 genomes]
rs73976160	0.95[AFR][1000 genomes]
rs73976164	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73976165	0.97[AFR][1000 genomes]
rs73976168	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73976170	0.83[AFR][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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172291000-172319800	Weak transcription	Stomach Mucosa	stomach
2	chr2:172291600-172311800	Weak transcription	Fetal Brain Male	brain
3	chr2:172291800-172338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:172292000-172312800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:172292000-172341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:172292600-172311600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:172292600-172312000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:172292600-172317600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:172292600-172320400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:172293000-172318600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:172293200-172311800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:172293200-172319400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:172293200-172319400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:172295000-172309600	Strong transcription	HepG2	liver
15	chr2:172295200-172309400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:172296600-172309600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:172297000-172313000	Weak transcription	A549	lung
18	chr2:172297000-172314000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:172298200-172310400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:172298200-172314200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:172298200-172326600	Weak transcription	Colonic Mucosa	Colon
22	chr2:172298400-172311800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:172298400-172314200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:172298400-172325400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:172298400-172325600	Weak transcription	Hela-S3	cervix
26	chr2:172298400-172326200	Weak transcription	NHEK	skin
27	chr2:172298400-172334400	Weak transcription	Small Intestine	intestine
28	chr2:172298400-172339400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:172298600-172341400	Weak transcription	NHLF	lung
30	chr2:172299400-172325400	Weak transcription	Gastric	stomach
31	chr2:172300600-172307800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:172300600-172338600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr2:172301600-172310600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:172303000-172307600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:172303400-172310600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:172303600-172307800	Strong transcription	Left Ventricle	heart
37	chr2:172303600-172310200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:172303600-172310600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:172303600-172316200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:172303600-172317000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:172303800-172307600	Strong transcription	HUVEC	blood vessel
42	chr2:172303800-172307600	Strong transcription	Osteobl	bone
43	chr2:172303800-172307800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:172303800-172307800	Strong transcription	Right Ventricle	heart
45	chr2:172303800-172308000	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:172303800-172308400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:172303800-172309600	Strong transcription	Adipose Nuclei	Adipose
48	chr2:172303800-172311600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr2:172303800-172312200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:172303800-172317400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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