Variant report

Variant	rs2045554
Chromosome Location	chr3:48494542-48494543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48493504..48495133-chr3:48498542..48501507,2	K562	blood:
2	chr3:48486792..48490170-chr3:48491410..48494926,8	MCF-7	breast:
3	chr3:48492997..48495746-chr3:48499460..48501743,2	MCF-7	breast:
4	chr3:48486214..48489756-chr3:48493754..48497547,4	K562	blood:
5	chr3:48486535..48489941-chr3:48491977..48496128,7	MCF-7	breast:
6	chr3:48485548..48495296-chr3:48503776..48510303,13	MCF-7	breast:
7	chr3:48493355..48497558-chr3:48502892..48507335,5	K562	blood:

Variant related genes	Relation type
ENSG00000164053	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000213689	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1037773	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10470686	0.94[EUR][1000 genomes]
rs1109227	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130170	0.94[EUR][1000 genomes]
rs11130171	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11712561	0.92[EUR][1000 genomes]
rs11797	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12487542	0.92[EUR][1000 genomes]
rs13069724	0.94[EUR][1000 genomes]
rs13071337	0.93[EUR][1000 genomes]
rs13072012	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13076076	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13091785	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314659	0.94[EUR][1000 genomes]
rs13324374	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1459242	0.88[EUR][1000 genomes]
rs1459249	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1459250	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1563736	0.93[EUR][1000 genomes]
rs1824363	0.99[ASN][1000 genomes]
rs1870444	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1975844	0.93[EUR][1000 genomes]
rs2242150	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279077	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290822	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362450	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2362452	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28824259	0.93[EUR][1000 genomes]
rs2885509	0.89[EUR][1000 genomes]
rs2885510	0.89[EUR][1000 genomes]
rs3214041	0.94[EUR][1000 genomes]
rs34761139	0.93[EUR][1000 genomes]
rs35215722	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774808	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4490383	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858793	0.89[EUR][1000 genomes]
rs4858795	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4858817	0.89[EUR][1000 genomes]
rs56298324	0.88[AFR][1000 genomes]
rs60512868	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442116	0.88[EUR][1000 genomes]
rs6442117	0.91[EUR][1000 genomes]
rs6442118	0.94[EUR][1000 genomes]
rs6442119	0.94[EUR][1000 genomes]
rs6442120	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442123	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442124	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764415	0.87[EUR][1000 genomes]
rs6770470	0.92[EUR][1000 genomes]
rs6776700	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6779262	0.89[EUR][1000 genomes]
rs6784322	0.91[EUR][1000 genomes]
rs6784541	0.91[EUR][1000 genomes]
rs6794875	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6796491	0.93[EUR][1000 genomes]
rs6800475	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804774	0.93[EUR][1000 genomes]
rs6810060	0.92[EUR][1000 genomes]
rs7126	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725309	0.89[EUR][1000 genomes]
rs725310	0.89[EUR][1000 genomes]
rs73074358	0.92[EUR][1000 genomes]
rs7618883	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7630741	0.89[EUR][1000 genomes]
rs7634377	0.91[EUR][1000 genomes]
rs7635522	0.92[EUR][1000 genomes]
rs7636044	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636782	0.90[EUR][1000 genomes]
rs7639743	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7653691	0.90[EUR][1000 genomes]
rs898225	0.88[EUR][1000 genomes]
rs922075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311423	0.91[EUR][1000 genomes]
rs9311424	0.91[EUR][1000 genomes]
rs9809843	0.93[EUR][1000 genomes]
rs9812647	0.94[EUR][1000 genomes]
rs9815103	0.89[EUR][1000 genomes]
rs9817615	0.95[ASN][1000 genomes]
rs9826195	0.93[EUR][1000 genomes]
rs9826247	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838618	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849509	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862575	0.93[EUR][1000 genomes]
rs9864371	0.93[EUR][1000 genomes]
rs9864815	0.93[EUR][1000 genomes]
rs9875280	0.93[EUR][1000 genomes]
rs9876781	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876891	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9881491	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883759	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9883927	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2045554	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs2045554	TMA7	cis	Muscle Skeletal	GTEx
rs2045554	TREX1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48489200-48494600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:48489200-48494800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:48489200-48498800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:48489200-48506200	Weak transcription	Stomach Mucosa	stomach
5	chr3:48489200-48507400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:48489400-48494600	Weak transcription	Brain Angular Gyrus	brain
7	chr3:48489400-48494600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:48489400-48494600	Weak transcription	Fetal Kidney	kidney
9	chr3:48489400-48494600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:48489400-48494600	Weak transcription	HSMMtube	muscle
11	chr3:48489400-48494600	Weak transcription	NHLF	lung
12	chr3:48489400-48494800	Weak transcription	Pancreas	Pancrea
13	chr3:48489400-48494800	Weak transcription	Small Intestine	intestine
14	chr3:48489400-48498600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:48489400-48500200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:48489400-48500200	Weak transcription	Colonic Mucosa	Colon
17	chr3:48489400-48500800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:48489600-48494600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:48489600-48494800	Weak transcription	A549	lung
20	chr3:48489600-48495000	Weak transcription	NHDF-Ad	bronchial
21	chr3:48489600-48500600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:48489600-48506400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:48489800-48506600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:48490400-48494600	Weak transcription	Hela-S3	cervix
25	chr3:48490400-48495000	Weak transcription	HUVEC	blood vessel
26	chr3:48490400-48498400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:48491000-48503200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:48491400-48503000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:48491400-48503000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:48491400-48503200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:48491400-48503200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:48491400-48506600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:48491600-48497600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:48491600-48500400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:48491600-48502600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:48491600-48503000	Strong transcription	Adipose Nuclei	Adipose
37	chr3:48491600-48503200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:48491800-48503200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:48491800-48506400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:48492000-48495200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:48492000-48499200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:48492000-48500200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:48492000-48500200	Strong transcription	Placenta	Placenta
44	chr3:48492000-48503200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:48492000-48503200	Strong transcription	Liver	Liver
46	chr3:48492000-48503600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:48492200-48503200	Strong transcription	Thymus	Thymus
48	chr3:48492200-48503400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:48492200-48503400	Strong transcription	Fetal Stomach	stomach
50	chr3:48492400-48496800	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links