Variant report

Variant	rs7958546
Chromosome Location	chr12:42979737-42979738
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	chr12:42978457..42981553-chr12:42981984..42984862,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139174	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10785350	0.95[ASN][1000 genomes]
rs10785351	0.90[EUR][1000 genomes]
rs10880320	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10880322	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11181563	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11181567	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181568	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11181570	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181571	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181575	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11837158	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12229911	0.84[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12370911	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1922758	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42960400-42981400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:42971000-42981400	Weak transcription	Stomach Mucosa	stomach
3	chr12:42975000-42981200	Enhancers	Fetal Stomach	stomach
4	chr12:42975600-42979800	Enhancers	Brain Germinal Matrix	brain
5	chr12:42976200-42980400	Enhancers	Fetal Muscle Leg	muscle
6	chr12:42976600-42981400	Enhancers	Fetal Lung	lung
7	chr12:42977200-42980600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:42977400-42981200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr12:42977600-42979800	Enhancers	Psoas Muscle	Psoas
10	chr12:42977800-42981000	Weak transcription	Brain Angular Gyrus	brain
11	chr12:42978000-42980000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:42978400-42979800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:42978400-42979800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:42978400-42979800	Enhancers	Right Atrium	heart
15	chr12:42978400-42980000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:42978400-42980000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:42978400-42981200	Active TSS	Fetal Kidney	kidney
18	chr12:42978600-42979800	Enhancers	Left Ventricle	heart
19	chr12:42978600-42979800	Enhancers	Right Ventricle	heart
20	chr12:42978600-42980800	Enhancers	HMEC	breast
21	chr12:42978600-42981200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:42978800-42979800	Enhancers	Adipose Nuclei	Adipose
23	chr12:42978800-42980000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:42978800-42980600	Enhancers	NHEK	skin
25	chr12:42978800-42980800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:42978800-42981000	Weak transcription	Fetal Brain Female	brain
27	chr12:42978800-42981200	Weak transcription	NHLF	lung
28	chr12:42978800-42981400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:42979000-42979800	Enhancers	Ovary	ovary
30	chr12:42979000-42979800	Genic enhancers	Osteobl	bone
31	chr12:42979000-42980000	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr12:42979000-42980000	Flanking Active TSS	NH-A	brain
33	chr12:42979000-42980200	Enhancers	Colon Smooth Muscle	Colon
34	chr12:42979000-42980200	Enhancers	Rectal Smooth Muscle	rectum
35	chr12:42979200-42979800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:42979200-42979800	Transcr. at gene 5' and 3'	HSMM	muscle
37	chr12:42979200-42979800	Flanking Active TSS	HSMMtube	muscle
38	chr12:42979200-42980000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:42979200-42980000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:42979200-42980200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:42979200-42980200	Flanking Active TSS	Fetal Heart	heart
42	chr12:42979200-42981600	Flanking Active TSS	HUVEC	blood vessel
43	chr12:42979400-42979800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:42979400-42979800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:42979400-42979800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:42979400-42979800	Enhancers	Aorta	Aorta
47	chr12:42979400-42979800	Enhancers	Placenta	Placenta
48	chr12:42979400-42979800	Enhancers	Lung	lung
49	chr12:42979400-42980000	Enhancers	H9 Cell Line	embryonic stem cell
50	chr12:42979400-42980000	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links