Variant report

Variant	rs58460482
Chromosome Location	chr3:45994388-45994389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:45992659..45994641-chr3:46028942..46030792,2	K562	blood:
2	chr3:45992876..45995243-chr3:45997512..46000332,2	K562	blood:
3	chr3:45992901..45995659-chr3:45998923..46000689,2	K562	blood:

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10049103	0.82[AMR][1000 genomes]
rs1078355	0.82[AMR][1000 genomes]
rs12107160	0.82[AMR][1000 genomes]
rs17078464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1873615	0.82[AMR][1000 genomes]
rs2036294	0.82[AMR][1000 genomes]
rs2036296	0.82[AMR][1000 genomes]
rs2088691	0.82[AMR][1000 genomes]
rs28393246	0.82[AMR][1000 genomes]
rs34147726	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs55743140	0.82[AMR][1000 genomes]
rs56071453	0.82[AMR][1000 genomes]
rs56239523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56738797	0.82[AMR][1000 genomes]
rs56972507	0.91[AMR][1000 genomes]
rs57036895	0.81[AMR][1000 genomes]
rs57161310	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs57228214	1.00[AMR][1000 genomes]
rs57768435	0.82[AMR][1000 genomes]
rs57800045	0.82[AMR][1000 genomes]
rs58050797	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58139750	0.82[AMR][1000 genomes]
rs58442576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58491168	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58969771	0.82[AMR][1000 genomes]
rs59754516	0.82[AMR][1000 genomes]
rs60080146	0.82[AMR][1000 genomes]
rs60110056	0.91[AMR][1000 genomes]
rs60431156	0.91[AMR][1000 genomes]
rs60445435	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs61201782	0.82[AMR][1000 genomes]
rs61276379	0.82[AMR][1000 genomes]
rs61598729	0.82[AMR][1000 genomes]
rs6788758	0.82[AMR][1000 genomes]
rs6791693	0.91[AMR][1000 genomes]
rs72885402	0.82[AMR][1000 genomes]
rs72887108	0.82[AMR][1000 genomes]
rs72887131	0.82[AMR][1000 genomes]
rs72889737	0.82[AMR][1000 genomes]
rs72889759	0.82[AMR][1000 genomes]
rs72891712	1.00[AMR][1000 genomes]
rs72899100	0.82[AMR][1000 genomes]
rs73830713	0.82[AMR][1000 genomes]
rs73833519	0.82[AMR][1000 genomes]
rs7619256	0.91[AMR][1000 genomes]
rs7627147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7638236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9852295	0.82[AMR][1000 genomes]
rs9859291	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:45981000-45999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
6	chr3:45982200-45999800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr3:45982800-46000800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:45983200-46012400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:45984400-45998200	Strong transcription	Left Ventricle	heart
10	chr3:45984400-46000800	Weak transcription	Psoas Muscle	Psoas
11	chr3:45986200-45998200	Strong transcription	Brain Substantia Nigra	brain
12	chr3:45986200-46006800	Strong transcription	Fetal Intestine Small	intestine
13	chr3:45986200-46007600	Strong transcription	Fetal Stomach	stomach
14	chr3:45986400-45997000	Strong transcription	Pancreas	Pancrea
15	chr3:45986400-45997200	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr3:45986400-46001400	Weak transcription	A549	lung
17	chr3:45986400-46006200	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:45986400-46006800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr3:45986400-46007600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:45986400-46012200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:45986600-45997000	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr3:45986600-45997000	Strong transcription	Brain Angular Gyrus	brain
24	chr3:45986600-45997400	Strong transcription	Brain Cingulate Gyrus	brain
25	chr3:45986600-46009000	Strong transcription	Primary B cells from cord blood	blood
26	chr3:45986600-46012000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:45986800-46012200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:45987000-45997600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:45987200-46013600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:45987600-45998200	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr3:45987600-46002000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:45987600-46007800	Strong transcription	K562	blood
36	chr3:45987800-45995600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:45987800-45997400	Strong transcription	Brain Anterior Caudate	brain
38	chr3:45987800-45997600	Strong transcription	Brain Hippocampus Middle	brain
39	chr3:45987800-46001400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:45987800-46012200	Strong transcription	HepG2	liver
41	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:45988000-45997000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:45988000-45997000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:45988000-45997600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:45988000-45999400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:45988000-46012000	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr3:45988000-46026600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:45988200-46009800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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