Variant report

Variant	rs2493419
Chromosome Location	chr1:120485517-120485518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120478050..120480567-chr1:120483456..120486194,2	MCF-7	breast:
2	chr1:120478510..120480187-chr1:120484617..120486258,2	K562	blood:
3	chr1:120485036..120488098-chr1:120488284..120491170,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134250	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10494235	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923926	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923929	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493695	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493696	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493698	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453042	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453044	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453055	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453056	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2487568	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493398	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493410	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493411	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493416	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2493420	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641316	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641338	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793823	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793827	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793830	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4659250	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025718	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688004	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs699780	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835573	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835574	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947273	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1816057	chr1:120469050-120697156	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv1818054	chr1:120469050-120697156	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1844863	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv1850218	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv427730	chr1:120469050-120697156	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120452000-120485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:120455800-120486800	Strong transcription	Liver	Liver
3	chr1:120456200-120488000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:120468400-120495800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:120468400-120506200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:120468400-120507400	Weak transcription	Right Ventricle	heart
7	chr1:120468600-120496000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:120468600-120532800	Weak transcription	Stomach Mucosa	stomach
9	chr1:120469600-120485600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:120475600-120485600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:120476400-120507400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:120476800-120485600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:120476800-120486000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:120476800-120488800	Strong transcription	Primary B cells from cord blood	blood
15	chr1:120477000-120486600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:120477000-120497200	Weak transcription	Small Intestine	intestine
17	chr1:120477400-120488000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:120478800-120508800	Weak transcription	A549	lung
19	chr1:120478800-120511000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:120479000-120511000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:120479200-120490800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:120479200-120491000	Weak transcription	Fetal Brain Male	brain
23	chr1:120479600-120493000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:120479600-120504000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:120480400-120507800	Weak transcription	Fetal Brain Female	brain
26	chr1:120480600-120490000	Weak transcription	Brain Germinal Matrix	brain
27	chr1:120480600-120490800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:120480600-120490800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:120480600-120490800	Weak transcription	HepG2	liver
30	chr1:120480600-120491000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:120480600-120492400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:120480600-120492600	Weak transcription	HUVEC	blood vessel
33	chr1:120480600-120495000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:120480600-120503600	Weak transcription	Brain Substantia Nigra	brain
35	chr1:120480600-120507400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:120480800-120488400	Weak transcription	Fetal Heart	heart
37	chr1:120482600-120490800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:120482600-120490800	Weak transcription	Hela-S3	cervix
39	chr1:120482800-120489800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:120482800-120490800	Weak transcription	Fetal Thymus	thymus
41	chr1:120483200-120490000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:120483400-120490200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:120483400-120490800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:120483400-120490800	Weak transcription	Fetal Intestine Small	intestine
45	chr1:120483400-120490800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:120483400-120490800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:120483400-120492600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:120483600-120488400	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:120483600-120490000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:120483600-120490200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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