Variant report

Variant	rs12046438
Chromosome Location	chr1:223924545-223924546
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223919205..223921124-chr1:223921422..223926352,4	K562	blood:
2	chr1:223906912..223908483-chr1:223923323..223925771,2	MCF-7	breast:
3	chr1:223924368..223926769-chr1:223968941..223970904,2	K562	blood:
4	chr1:223898969..223903164-chr1:223924094..223928992,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12022934	1.00[ASN][1000 genomes]
rs12023822	1.00[ASN][1000 genomes]
rs12025088	0.90[ASN][1000 genomes]
rs12034645	0.84[ASN][1000 genomes]
rs12036573	0.84[ASN][1000 genomes]
rs12037507	1.00[ASN][1000 genomes]
rs12048989	0.90[ASN][1000 genomes]
rs1222142	0.85[ASN][1000 genomes]
rs28370041	1.00[ASN][1000 genomes]
rs59206866	0.98[ASN][1000 genomes]
rs8179303	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking 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	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915200-223930800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223915400-223927200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:223915800-223931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:223916600-223927000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:223916600-223932600	Weak transcription	Fetal Brain Female	brain
9	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:223919600-223924800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:223919800-223924800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:223919800-223925000	Weak transcription	HSMMtube	muscle
14	chr1:223919800-223926000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:223919800-223931200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:223921200-223924800	Weak transcription	Placenta	Placenta
17	chr1:223921200-223927800	Genic enhancers	A549	lung
18	chr1:223921200-223932800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:223921200-223936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:223921400-223926000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:223921400-223931400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:223921600-223926000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:223921600-223926000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:223921600-223926200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:223921600-223932800	Weak transcription	Liver	Liver
26	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:223921800-223924800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:223921800-223925400	Genic enhancers	Lung	lung
29	chr1:223921800-223926000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:223921800-223933400	Weak transcription	Brain Angular Gyrus	brain
31	chr1:223921800-223935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:223921800-223936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:223922200-223925800	Weak transcription	Fetal Kidney	kidney
34	chr1:223922200-223926200	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:223922200-223926400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:223922200-223934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:223922200-223935600	Weak transcription	Fetal Brain Male	brain
38	chr1:223922400-223924800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:223922400-223924800	Weak transcription	Aorta	Aorta
40	chr1:223922400-223924800	Weak transcription	Colonic Mucosa	Colon
41	chr1:223922400-223924800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:223922400-223925000	Weak transcription	Pancreas	Pancrea
43	chr1:223922400-223925200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:223922400-223925200	Strong transcription	NHLF	lung
45	chr1:223922400-223926200	Weak transcription	NHDF-Ad	bronchial
46	chr1:223922400-223926600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:223922400-223927400	Weak transcription	Small Intestine	intestine
48	chr1:223922400-223927800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr1:223922600-223926200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:223922600-223927200	Weak transcription	Fetal Lung	lung

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