Variant report

Variant	rs12126625
Chromosome Location	chr1:179831963-179831964
allele	C/T
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:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179821213..179823373-chr1:179831118..179833958,2	K562	blood:
2	chr1:179827853..179829616-chr1:179831042..179832736,2	K562	blood:
3	chr1:179831047..179833127-chr1:179833809..179835853,2	MCF-7	breast:
4	chr1:179808933..179811748-chr1:179830846..179833162,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOR1AIP1-2	chr1:179831573-179832371	ENSG00000245075
2	lnc-AL359853.2-2	chr1:179831573-179832347	NONHSAT008218

No data

Variant related genes	Relation type
ENSG00000258664	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1048418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494523	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913894	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913895	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913905	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10913909	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12119431	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12121694	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136091	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12136465	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12143942	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12144991	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16854910	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3845388	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4301600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61740391	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6425596	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6659939	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6673144	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72708661	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72708662	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7527215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7531195	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7545581	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7549317	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9726605	1.00[AMR][1000 genomes];0.99[EUR][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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv528201	chr1:179831248-179832643	Strong transcription Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv519273	chr1:179831248-179847877	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179802400-179836200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:179803600-179833600	Weak transcription	Fetal Brain Male	brain
4	chr1:179807800-179833800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:179808600-179837000	Strong transcription	Liver	Liver
6	chr1:179808600-179839800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:179808800-179836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:179812600-179842600	Weak transcription	Stomach Mucosa	stomach
9	chr1:179813200-179839200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:179813400-179834000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:179814200-179834400	Weak transcription	Fetal Heart	heart
12	chr1:179814400-179839200	Strong transcription	HSMM	muscle
13	chr1:179815000-179839400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:179816000-179836000	Weak transcription	Colonic Mucosa	Colon
15	chr1:179820200-179834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:179820400-179832200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:179820400-179833600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:179820400-179834000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:179820400-179841400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:179820400-179841800	Weak transcription	Small Intestine	intestine
21	chr1:179820400-179844200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:179820400-179845400	Weak transcription	Right Ventricle	heart
23	chr1:179820600-179832600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:179820600-179832800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:179820600-179834000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:179820600-179834000	Weak transcription	HSMMtube	muscle
27	chr1:179821000-179833400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:179821000-179833600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:179821000-179833600	Weak transcription	Fetal Kidney	kidney
30	chr1:179821000-179834200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:179821200-179832400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:179821200-179834000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:179821800-179832600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:179823000-179839200	Strong transcription	Osteobl	bone
35	chr1:179823800-179839200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:179823800-179843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:179824200-179839800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:179824400-179837800	Strong transcription	Primary B cells from cord blood	blood
39	chr1:179824600-179838400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:179825000-179838200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:179825600-179833000	Strong transcription	Fetal Intestine Small	intestine
42	chr1:179825600-179839000	Strong transcription	Fetal Intestine Large	intestine
43	chr1:179825800-179839200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:179826000-179832600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:179826200-179843400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:179826600-179832400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:179826600-179832400	Weak transcription	Lung	lung
48	chr1:179826600-179834400	Weak transcription	Spleen	Spleen
49	chr1:179826800-179832200	Weak transcription	NHEK	skin
50	chr1:179826800-179832600	Weak transcription	Fetal Lung	lung

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