Variant report

Variant	rs3741429
Chromosome Location	chr12:11922680-11922681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11801832..11803757-chr12:11920063..11922984,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

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

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

rs_ID	r²[population]
rs2051523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2723827	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2723828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2723830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2724594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2724658	0.87[EUR][1000 genomes]
rs2856327	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3782140	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488451	0.82[EUR][1000 genomes]
rs7961094	0.87[EUR][1000 genomes]
rs7967177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	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
3	nsv469113	chr12:11913360-11931259	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv557574	chr12:11913360-11931259	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv469114	chr12:11916908-11929481	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv557575	chr12:11916908-11929481	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11908600-11931800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:11909600-11932400	Genic enhancers	Fetal Thymus	thymus
3	chr12:11914400-11925400	Genic enhancers	Dnd41	blood
4	chr12:11914400-11925800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:11914800-11923600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr12:11915400-11938000	Weak transcription	NHEK	skin
7	chr12:11915600-11938000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:11918000-11923600	Enhancers	Adipose Nuclei	Adipose
9	chr12:11918000-11923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:11918000-11936000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:11919000-11923200	Weak transcription	Right Ventricle	heart
12	chr12:11919000-11923400	Enhancers	Duodenum Mucosa	Duodenum
13	chr12:11919400-11923800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:11919400-11926800	Enhancers	Primary hematopoietic stem cells	blood
15	chr12:11919400-11935000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:11919600-11922800	Weak transcription	Esophagus	oesophagus
17	chr12:11919600-11924000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:11919600-11926800	Weak transcription	Psoas Muscle	Psoas
19	chr12:11919600-11927600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:11919600-11932000	Weak transcription	HSMM	muscle
21	chr12:11919600-11936200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:11919600-11936800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:11919800-11922800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:11919800-11922800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:11919800-11922800	Weak transcription	Placenta	Placenta
26	chr12:11919800-11923000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:11919800-11924000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr12:11919800-11926600	Weak transcription	Brain Anterior Caudate	brain
29	chr12:11919800-11927600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:11919800-11929400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:11919800-11931400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:11919800-11932400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:11920000-11922800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:11920000-11922800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:11920000-11923000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:11920000-11924200	Weak transcription	Osteobl	bone
37	chr12:11920000-11924400	Weak transcription	NH-A	brain
38	chr12:11920000-11924800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:11920000-11924800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:11920000-11926400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr12:11920000-11927800	Weak transcription	Brain Substantia Nigra	brain
42	chr12:11920000-11929600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:11920000-11931800	Weak transcription	HSMMtube	muscle
44	chr12:11920000-11937800	Weak transcription	NHLF	lung
45	chr12:11920200-11924400	Weak transcription	HMEC	breast
46	chr12:11920200-11926600	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:11920400-11922800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr12:11920600-11922800	Weak transcription	Lung	lung
49	chr12:11920600-11924000	Genic enhancers	GM12878-XiMat	blood
50	chr12:11920600-11926800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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