Variant report

Variant	rs11054960
Chromosome Location	chr12:12690235-12690236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12684001..12705444-chr12:12707828..12718639,50	MCF-7	breast:
2	chr12:12418787..12421715-chr12:12690160..12692960,2	MCF-7	breast:
3	chr12:12688605..12691536-chr12:12762054..12764846,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000111269	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10845573	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11054950	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11054961	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054965	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12308450	0.93[AMR][1000 genomes]
rs12309782	0.93[AMR][1000 genomes]
rs12309848	0.93[AMR][1000 genomes]
rs4421828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58968872	0.93[AMR][1000 genomes]
rs7138733	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295113	0.93[AMR][1000 genomes]
rs7309871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12664000-12690400	Weak transcription	NHLF	lung
2	chr12:12672800-12691200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:12674200-12691200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:12681400-12693600	Weak transcription	Lung	lung
5	chr12:12682200-12691400	Weak transcription	Adipose Nuclei	Adipose
6	chr12:12682200-12693000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:12683400-12693600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:12685000-12692600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr12:12686600-12692200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:12686600-12693600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:12686600-12701000	Weak transcription	HSMM	muscle
12	chr12:12686600-12703200	Weak transcription	NH-A	brain
13	chr12:12686600-12708000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:12686600-12711400	Weak transcription	Esophagus	oesophagus
15	chr12:12686800-12691000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:12686800-12712200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:12686800-12712600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:12687000-12691000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:12687000-12691200	Weak transcription	Brain Anterior Caudate	brain
20	chr12:12687200-12692000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:12687200-12693800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:12687200-12698400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:12687200-12708000	Weak transcription	Right Ventricle	heart
24	chr12:12687200-12711600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:12687200-12712600	Weak transcription	Aorta	Aorta
26	chr12:12687400-12691000	Weak transcription	Psoas Muscle	Psoas
27	chr12:12687400-12691000	Weak transcription	Thymus	Thymus
28	chr12:12687400-12691200	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:12687400-12691400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:12687400-12691600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:12687400-12691600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:12687400-12692800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:12687400-12694000	Weak transcription	Fetal Stomach	stomach
34	chr12:12687400-12694200	Weak transcription	Placenta	Placenta
35	chr12:12687400-12706400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:12687400-12708000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:12687400-12708000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:12687400-12710600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:12687400-12712600	Weak transcription	K562	blood
40	chr12:12687600-12691000	Weak transcription	Fetal Lung	lung
41	chr12:12687600-12691200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:12687600-12691200	Weak transcription	A549	lung
43	chr12:12687600-12693400	Weak transcription	Primary T cells from cord blood	blood
44	chr12:12688200-12691000	Weak transcription	Brain Angular Gyrus	brain
45	chr12:12688200-12691000	Weak transcription	Left Ventricle	heart
46	chr12:12688200-12691200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:12688200-12691400	Weak transcription	Brain Substantia Nigra	brain
48	chr12:12688200-12691600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:12688200-12691600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:12688200-12691600	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links