Variant report

Variant	rs3219497
Chromosome Location	chr1:45795027-45795028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45791337..45793559-chr1:45793644..45795493,3	MCF-7	breast:
2	chr1:45794537..45798205-chr1:45802201..45806836,5	MCF-7	breast:
3	chr1:45284151..45285923-chr1:45793596..45795335,3	K562	blood:
4	chr1:45284151..45285923-chr1:45793815..45795335,2	K562	blood:
5	chr1:45794711..45795238-chr1:45805291..45805841,2	Hela-S3	cervix:
6	chr1:45240561..45242696-chr1:45794444..45796919,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200913	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000186603	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1007005	1.00[AMR][1000 genomes]
rs1561794	1.00[AMR][1000 genomes]
rs1892476	1.00[AMR][1000 genomes]
rs2211646	1.00[AMR][1000 genomes]
rs57755658	1.00[AMR][1000 genomes]
rs58600794	1.00[AMR][1000 genomes]
rs58829168	1.00[AMR][1000 genomes]
rs59089628	1.00[AMR][1000 genomes]
rs59351600	1.00[AMR][1000 genomes]
rs59975097	1.00[AMR][1000 genomes]
rs60789611	1.00[AMR][1000 genomes]
rs72890576	1.00[AMR][1000 genomes]
rs72890601	1.00[AMR][1000 genomes]
rs72892514	1.00[AMR][1000 genomes]
rs72892526	1.00[AMR][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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3219497	FAM153A	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45787200-45796600	Weak transcription	HepG2	liver
2	chr1:45792400-45800600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:45792800-45804800	Weak transcription	Fetal Kidney	kidney
4	chr1:45792800-45805000	Weak transcription	HSMMtube	muscle
5	chr1:45793000-45796000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:45793000-45796800	Weak transcription	HSMM	muscle
7	chr1:45793200-45795200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:45793200-45795800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:45793200-45796200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:45793200-45796600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:45793200-45796800	Weak transcription	Osteobl	bone
12	chr1:45793200-45797800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:45793200-45804800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:45793400-45795200	Weak transcription	Adipose Nuclei	Adipose
15	chr1:45793400-45795200	Enhancers	Esophagus	oesophagus
16	chr1:45793400-45795600	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:45793400-45795600	Flanking Active TSS	Hela-S3	cervix
18	chr1:45793400-45796600	Weak transcription	Right Ventricle	heart
19	chr1:45793400-45796800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:45793400-45796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:45793400-45796800	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:45793400-45803800	Weak transcription	Small Intestine	intestine
23	chr1:45793400-45804000	Weak transcription	HMEC	breast
24	chr1:45793400-45805000	Weak transcription	Right Atrium	heart
25	chr1:45793600-45795600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:45793600-45795800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:45793600-45796000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:45793600-45796600	Weak transcription	Primary B cells from cord blood	blood
29	chr1:45793600-45796600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:45793600-45796800	Weak transcription	Fetal Lung	lung
31	chr1:45793600-45797200	Weak transcription	Left Ventricle	heart
32	chr1:45793600-45797200	Enhancers	Stomach Mucosa	stomach
33	chr1:45793600-45800600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:45793600-45800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:45793600-45803600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:45793600-45803600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:45793600-45804200	Weak transcription	Fetal Brain Male	brain
38	chr1:45793800-45795200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:45793800-45795200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:45793800-45795400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:45793800-45795400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:45793800-45795400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:45793800-45796000	Weak transcription	Brain Anterior Caudate	brain
44	chr1:45793800-45796200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:45793800-45796800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:45793800-45796800	Weak transcription	Colonic Mucosa	Colon
47	chr1:45793800-45799800	Weak transcription	HUVEC	blood vessel
48	chr1:45793800-45803800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:45794000-45795200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:45794000-45795200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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