Variant report

Variant	rs11168938
Chromosome Location	chr12:49655598-49655599
allele	A/C
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	MAFK	chr12:49655383-49655877	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49653372..49655106-chr12:49655142..49656761,3	MCF-7	breast:
2	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:
3	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000135406	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000186897	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10047512	1.00[YRI][hapmap];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[ASW][hapmap];0.81[LWK][hapmap];1.00[AMR][1000 genomes]
rs11168931	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs11168939	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	0.94[LWK][hapmap];1.00[YRI][hapmap];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[ASW][hapmap];0.93[LWK][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12296536	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12297433	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12300386	1.00[AMR][1000 genomes]
rs12300998	1.00[AMR][1000 genomes]
rs12303188	0.87[YRI][hapmap]
rs12304259	1.00[ASW][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12304483	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304746	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs12308571	0.97[AFR][1000 genomes]
rs12309028	1.00[ASW][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];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[YRI][hapmap];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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11168938	NOTUM	trans	lymphoblastoid	seeQTL

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	chr12:49653200-49655600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:49653200-49656200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:49653200-49656400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:49653200-49657000	Enhancers	NHDF-Ad	bronchial
10	chr12:49653400-49656000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:49653600-49658000	Weak transcription	Fetal Kidney	kidney
12	chr12:49654000-49655600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:49654000-49656000	Enhancers	NHLF	lung
14	chr12:49654200-49658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:49654400-49655600	Weak transcription	K562	blood
16	chr12:49654400-49657000	Weak transcription	Hela-S3	cervix
17	chr12:49654400-49657000	Weak transcription	HSMM	muscle
18	chr12:49654400-49657200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:49654400-49657200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:49654400-49657400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:49654400-49657400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:49654600-49655600	Weak transcription	NH-A	brain
23	chr12:49654600-49656000	Enhancers	NHEK	skin
24	chr12:49654600-49656200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:49654600-49657000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:49654600-49657000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:49654600-49657000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:49654600-49657000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr12:49654600-49657200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:49654600-49657200	Weak transcription	Adipose Nuclei	Adipose
31	chr12:49654600-49657400	Enhancers	Osteobl	bone
32	chr12:49654600-49657800	Weak transcription	Fetal Lung	lung
33	chr12:49654600-49658000	Weak transcription	Aorta	Aorta
34	chr12:49654800-49655800	Weak transcription	Fetal Thymus	thymus
35	chr12:49654800-49656000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:49654800-49657000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:49654800-49657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:49654800-49657200	Weak transcription	HMEC	breast
39	chr12:49654800-49657200	Weak transcription	HUVEC	blood vessel
40	chr12:49654800-49657400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:49654800-49657600	Weak transcription	Primary B cells from cord blood	blood
42	chr12:49654800-49657800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:49654800-49658000	Weak transcription	Ovary	ovary
44	chr12:49655000-49656800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr12:49655000-49656800	Weak transcription	Fetal Muscle Leg	muscle
46	chr12:49655000-49656800	Weak transcription	Placenta	Placenta
47	chr12:49655000-49657200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:49655000-49658000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:49655000-49658200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:49655200-49655600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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