Variant report

Variant	rs11054961
Chromosome Location	chr12:12691728-12691729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:12684001..12705444-chr12:12707828..12718639,50	MCF-7	breast:
2	chr12:12685312..12688917-chr12:12690468..12693651,8	MCF-7	breast:
3	chr12:12418787..12421715-chr12:12690160..12692960,2	MCF-7	breast:
4	chr12:12690370..12694611-chr12:12733307..12736192,4	MCF-7	breast:
5	chr12:12690631..12694547-chr12:12695953..12699425,4	K562	blood:
6	chr12:12501929..12504054-chr12:12691121..12693736,2	MCF-7	breast:
7	chr12:12642881..12645570-chr12:12690793..12693318,2	MCF-7	breast:
8	chr12:12659166..12661033-chr12:12690816..12693581,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111261	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10845573	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11054927	0.90[MEX][hapmap]
rs11054931	1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11054938	1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11054950	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11054960	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054965	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12297678	0.89[YRI][hapmap]
rs12308450	0.93[AMR][1000 genomes]
rs12309339	1.00[MEX][hapmap];0.89[TSI][hapmap]
rs12309782	0.93[AMR][1000 genomes]
rs12309848	0.93[AMR][1000 genomes]
rs12581531	0.89[MEX][hapmap]
rs4421828	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[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	0.96[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961296	1.00[MEX][hapmap]

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	chr12:12681400-12693600	Weak transcription	Lung	lung
2	chr12:12682200-12693000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr12:12683400-12693600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:12685000-12692600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr12:12686600-12692200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:12686600-12693600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:12686600-12701000	Weak transcription	HSMM	muscle
8	chr12:12686600-12703200	Weak transcription	NH-A	brain
9	chr12:12686600-12708000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:12686600-12711400	Weak transcription	Esophagus	oesophagus
11	chr12:12686800-12712200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:12686800-12712600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:12687200-12692000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:12687200-12693800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:12687200-12698400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:12687200-12708000	Weak transcription	Right Ventricle	heart
17	chr12:12687200-12711600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:12687200-12712600	Weak transcription	Aorta	Aorta
19	chr12:12687400-12692800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:12687400-12694000	Weak transcription	Fetal Stomach	stomach
21	chr12:12687400-12694200	Weak transcription	Placenta	Placenta
22	chr12:12687400-12706400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:12687400-12708000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:12687400-12708000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:12687400-12710600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:12687400-12712600	Weak transcription	K562	blood
27	chr12:12687600-12693400	Weak transcription	Primary T cells from cord blood	blood
28	chr12:12688200-12693400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr12:12688200-12693400	Weak transcription	GM12878-XiMat	blood
30	chr12:12688200-12693600	Weak transcription	Right Atrium	heart
31	chr12:12688200-12694000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:12688200-12710800	Weak transcription	Pancreas	Pancrea
33	chr12:12688200-12714400	Weak transcription	Gastric	stomach
34	chr12:12688400-12695600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr12:12689000-12693400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:12689400-12692200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr12:12689400-12693400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:12689400-12694200	Weak transcription	HepG2	liver
39	chr12:12689600-12708000	Weak transcription	Ovary	ovary
40	chr12:12690400-12692600	Enhancers	Fetal Heart	heart
41	chr12:12690600-12692200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr12:12690600-12712600	Weak transcription	NHLF	lung
43	chr12:12690800-12693400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:12690800-12697400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:12690800-12710400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:12691000-12691800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:12691000-12692000	Enhancers	Brain Angular Gyrus	brain
48	chr12:12691000-12692000	Enhancers	Thymus	Thymus
49	chr12:12691000-12692400	Enhancers	Brain Hippocampus Middle	brain
50	chr12:12691000-12692600	Enhancers	Brain Cingulate Gyrus	brain

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