Variant report

Variant	rs4970918
Chromosome Location	chr1:150553348-150553349
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:150547986..150553838-chr1:150598744..150606232,19	K562	blood:
2	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
3	chr1:150548752..150555486-chr1:150599368..150605834,15	MCF-7	breast:
4	chr1:150547577..150553391-chr1:150562900..150573800,12	MCF-7	breast:
5	chr1:150551507..150553628-chr1:150668472..150670953,2	K562	blood:
6	chr1:150550164..150555275-chr1:150782862..150788394,7	MCF-7	breast:
7	chr1:150549744..150554023-chr1:150847608..150851573,5	K562	blood:
8	chr1:150521298..150527553-chr1:150548198..150553572,10	MCF-7	breast:
9	chr1:150550535..150554049-chr1:150976755..150981799,6	K562	blood:
10	chr1:150548124..150553459-chr1:150571951..150579395,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143420	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000143457	Chromatin interaction
ENSG00000253047	Chromatin interaction
ENSG00000264553	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000143437	Chromatin interaction
ENSG00000143363	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1053732	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888384	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888385	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204668	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204669	0.93[ASN][1000 genomes]
rs11204675	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204677	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204678	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204679	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204680	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204684	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11585169	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12116492	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125672	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126271	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12139563	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12406712	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12746899	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971378	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2048558	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738484	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738485	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754209	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970923	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971041	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55862611	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61820165	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669122	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6697620	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698495	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878471	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs932054	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9803935	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv535157	chr1:150552692-150575941	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4970918	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs4970918	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs4970918	ARNT	cis	Thyroid	GTEx
rs4970918	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs4970918	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs4970918	HORMAD1	cis	Nerve Tibial	GTEx
rs4970918	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs4970918	GOLPH3L	cis	Nerve Tibial	GTEx
rs4970918	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs4970918	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs4970918	HORMAD1	cis	Esophagus Mucosa	GTEx
rs4970918	RNU6-1042P	cis	Esophagus Mucosa	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150552000-150553800	Weak transcription	Gastric	stomach
2	chr1:150552400-150553400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:150552800-150553400	Enhancers	Pancreas	Pancrea
4	chr1:150552800-150553400	Enhancers	Small Intestine	intestine
5	chr1:150552800-150553800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr1:150552800-150554000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:150552800-150554000	Enhancers	Duodenum Mucosa	Duodenum
8	chr1:150552800-150554200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:150553000-150553400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:150553000-150553400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:150553000-150553400	Enhancers	Colonic Mucosa	Colon
12	chr1:150553000-150553400	Enhancers	Fetal Intestine Small	intestine
13	chr1:150553000-150553600	Weak transcription	HSMM	muscle
14	chr1:150553000-150553800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:150553000-150553800	Enhancers	Colon Smooth Muscle	Colon
16	chr1:150553000-150553800	Enhancers	Lung	lung
17	chr1:150553000-150553800	Enhancers	Stomach Mucosa	stomach
18	chr1:150553000-150554000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:150553000-150554000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:150553000-150554000	Enhancers	HSMMtube	muscle
21	chr1:150553000-150554000	Enhancers	K562	blood
22	chr1:150553000-150554800	Weak transcription	Primary T cells from cord blood	blood
23	chr1:150553000-150555000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:150553000-150555400	Enhancers	Primary B cells from peripheral blood	blood
25	chr1:150553000-150555600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:150553000-150556000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:150553000-150557000	Weak transcription	Fetal Stomach	stomach
28	chr1:150553000-150557200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:150553000-150559200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:150553000-150560600	Weak transcription	Right Atrium	heart
31	chr1:150553000-150562600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:150553000-150572800	Weak transcription	Thymus	Thymus
33	chr1:150553000-150583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:150553200-150553400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:150553200-150553400	Enhancers	Psoas Muscle	Psoas
36	chr1:150553200-150553400	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr1:150553200-150553800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:150553200-150553800	Enhancers	Adipose Nuclei	Adipose
39	chr1:150553200-150553800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:150553200-150553800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:150553200-150554000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:150553200-150554000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:150553200-150554000	Enhancers	Hela-S3	cervix
44	chr1:150553200-150554200	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr1:150553200-150554600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:150553200-150554600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:150553200-150554800	Weak transcription	Primary B cells from cord blood	blood
48	chr1:150553200-150554800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:150553200-150554800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:150553200-150554800	Weak transcription	Osteobl	bone

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