Variant report

Variant	rs11168939
Chromosome Location	chr12:49656380-49656381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr12:49656061-49656433	GM12878	blood:	n/a	chr12:49656235-49656252 chr12:49656233-49656251
2	CTCF	chr12:49656260-49656410	GM12872	blood:	n/a	n/a
3	PAX5	chr12:49656040-49656421	GM12878	blood:	n/a	chr12:49656235-49656252 chr12:49656233-49656251
4	ZNF384	chr12:49656021-49656403	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49523107..49527860-chr12:49656151..49664210,14	MCF-7	breast:
2	chr12:49519590..49527322-chr12:49655772..49662610,57	K562	blood:
3	chr12:49653372..49655106-chr12:49655142..49656761,3	MCF-7	breast:
4	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
5	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:
6	chr12:49522979..49526796-chr12:49655970..49661455,13	MCF-7	breast:
7	chr12:49410741..49414968-chr12:49656213..49660641,6	K562	blood:
8	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000181929	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000200309	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10047512	1.00[AMR][1000 genomes]
rs10047588	1.00[AMR][1000 genomes]
rs1109811	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168925	1.00[AMR][1000 genomes]
rs11168927	1.00[AMR][1000 genomes]
rs11168928	1.00[AMR][1000 genomes]
rs11168931	1.00[AMR][1000 genomes]
rs11168938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168952	0.89[AFR][1000 genomes]
rs11168954	0.89[AFR][1000 genomes]
rs11168955	0.86[AFR][1000 genomes]
rs11168956	0.97[AFR][1000 genomes]
rs11168957	0.97[AFR][1000 genomes]
rs11168958	0.97[AFR][1000 genomes]
rs12296231	1.00[AMR][1000 genomes]
rs12296536	1.00[AMR][1000 genomes]
rs12297433	1.00[AMR][1000 genomes]
rs12300386	1.00[AMR][1000 genomes]
rs12300998	1.00[AMR][1000 genomes]
rs12304259	1.00[AMR][1000 genomes]
rs12304483	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304746	1.00[AMR][1000 genomes]
rs12308571	0.97[AFR][1000 genomes]
rs12309028	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310093	0.89[AFR][1000 genomes]
rs12314967	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318666	1.00[AMR][1000 genomes]
rs12322876	1.00[AMR][1000 genomes]
rs28758893	1.00[AMR][1000 genomes]
rs3759170	0.89[AFR][1000 genomes]
rs9804936	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49629400-49657800	Weak transcription	Fetal Stomach	stomach
2	chr12:49650000-49657200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr12:49650000-49658000	Weak transcription	Right Atrium	heart
4	chr12:49652000-49656800	Weak transcription	HepG2	liver
5	chr12:49652200-49658000	Weak transcription	Fetal Brain Female	brain
6	chr12:49653200-49656400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:49653200-49657000	Enhancers	NHDF-Ad	bronchial
8	chr12:49653600-49658000	Weak transcription	Fetal Kidney	kidney
9	chr12:49654200-49658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:49654400-49657000	Weak transcription	Hela-S3	cervix
11	chr12:49654400-49657000	Weak transcription	HSMM	muscle
12	chr12:49654400-49657200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:49654400-49657200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:49654400-49657400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:49654400-49657400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:49654600-49657000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:49654600-49657000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:49654600-49657000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:49654600-49657000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:49654600-49657200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:49654600-49657200	Weak transcription	Adipose Nuclei	Adipose
22	chr12:49654600-49657400	Enhancers	Osteobl	bone
23	chr12:49654600-49657800	Weak transcription	Fetal Lung	lung
24	chr12:49654600-49658000	Weak transcription	Aorta	Aorta
25	chr12:49654800-49657000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:49654800-49657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:49654800-49657200	Weak transcription	HMEC	breast
28	chr12:49654800-49657200	Weak transcription	HUVEC	blood vessel
29	chr12:49654800-49657400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:49654800-49657600	Weak transcription	Primary B cells from cord blood	blood
31	chr12:49654800-49657800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:49654800-49658000	Weak transcription	Ovary	ovary
33	chr12:49655000-49656800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr12:49655000-49656800	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:49655000-49656800	Weak transcription	Placenta	Placenta
36	chr12:49655000-49657200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:49655000-49658000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:49655000-49658200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:49655600-49657000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:49655600-49657000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:49655600-49657000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:49655800-49657000	Weak transcription	A549	lung
43	chr12:49655800-49657000	Weak transcription	K562	blood
44	chr12:49655800-49657200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:49655800-49657400	Enhancers	Fetal Thymus	thymus
46	chr12:49656000-49657000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:49656000-49657000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:49656000-49657000	Weak transcription	NH-A	brain
49	chr12:49656000-49657000	Weak transcription	NHEK	skin
50	chr12:49656000-49657000	Weak transcription	NHLF	lung

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