Variant report

Variant	rs1547393
Chromosome Location	chr12:11910392-11910393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11801321..11803340-chr12:11910245..11911910,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11054443	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs11615083	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12425912	0.84[AMR][1000 genomes]
rs17210559	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2051524	0.81[EUR][1000 genomes]
rs3782137	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3825082	0.81[CEU][hapmap]
rs4763723	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs928950	0.84[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:11895000-11912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:11895400-11914400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:11900400-11910600	Weak transcription	Colonic Mucosa	Colon
6	chr12:11900600-11915000	Weak transcription	NHEK	skin
7	chr12:11901400-11911000	Weak transcription	Fetal Lung	lung
8	chr12:11902800-11910600	Weak transcription	Brain Angular Gyrus	brain
9	chr12:11902800-11910600	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:11902800-11910600	Weak transcription	Brain Substantia Nigra	brain
11	chr12:11903400-11910400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:11904000-11918000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:11904200-11913000	Strong transcription	Dnd41	blood
14	chr12:11904400-11910600	Genic enhancers	GM12878-XiMat	blood
15	chr12:11905200-11910400	Strong transcription	Fetal Stomach	stomach
16	chr12:11905200-11911400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:11905400-11910800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:11905400-11911600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:11905800-11918400	Weak transcription	Fetal Brain Male	brain
20	chr12:11906000-11912000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:11906200-11910600	Weak transcription	Esophagus	oesophagus
22	chr12:11906200-11911000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:11906400-11910400	Strong transcription	Primary B cells from cord blood	blood
24	chr12:11906400-11911000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:11906400-11911200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:11906400-11918600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:11906600-11910600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:11906600-11911400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:11906600-11911400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:11906800-11911000	Weak transcription	Stomach Mucosa	stomach
31	chr12:11906800-11911600	Weak transcription	Gastric	stomach
32	chr12:11906800-11915000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:11906800-11915000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:11907000-11910400	Weak transcription	Spleen	Spleen
35	chr12:11907000-11910600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:11907000-11917200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:11907200-11910400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:11907200-11911200	Weak transcription	Pancreas	Pancrea
39	chr12:11907200-11914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:11907400-11910600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:11907600-11911000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:11907600-11918200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr12:11907800-11910600	Weak transcription	Right Ventricle	heart
44	chr12:11907800-11910800	Weak transcription	Aorta	Aorta
45	chr12:11907800-11915000	Weak transcription	HMEC	breast
46	chr12:11908000-11910600	Weak transcription	Placenta	Placenta
47	chr12:11908000-11912600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr12:11908000-11913000	Enhancers	Fetal Heart	heart
49	chr12:11908000-11918800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:11908200-11910600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links