Variant report

Variant	rs11042911
Chromosome Location	chr11:10678785-10678786
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	BATF	chr11:10678767-10679329	GM12878	blood:	n/a	n/a
2	YY1	chr11:10678668-10679683	GM12878	blood:	n/a	chr11:10678919-10678941
3	TBL1XR1	chr11:10678612-10679255	K562	blood:	n/a	n/a
4	POLR2A	chr11:10678774-10679534	GM12892	blood:	n/a	n/a
5	MTA3	chr11:10678684-10679824	GM12878	blood:	n/a	n/a
6	PBX3	chr11:10678740-10678933	GM12878	blood:	n/a	n/a
7	FOXM1	chr11:10678784-10679425	GM12878	blood:	n/a	n/a
8	RUNX3	chr11:10678762-10679718	GM12878	blood:	n/a	n/a
9	ZNF143	chr11:10678721-10680275	GM12878	blood:	n/a	n/a
10	STAT3	chr11:10678676-10679435	GM12878	blood:	n/a	chr11:10679149-10679160
11	NR2F2	chr11:10678690-10679849	K562	blood:	n/a	n/a
12	PML	chr11:10678733-10679475	GM12878	blood:	n/a	n/a
13	UBTF	chr11:10678699-10678793	K562	blood:	n/a	n/a
14	CBX3	chr11:10678671-10679727	K562	blood:	n/a	n/a
15	STAT5A	chr11:10678668-10679353	GM12878	blood:	n/a	n/a
16	RUNX3	chr11:10678649-10679531	GM12878	blood:	n/a	n/a
17	JUN	chr11:10678389-10682546	K562	blood:	n/a	chr11:10681439-10681449 chr11:10679139-10679149 chr11:10681462-10681474 chr11:10679139-10679149 chr11:10681463-10681473 chr11:10679140-10679148 chr11:10679139-10679149 chr11:10681464-10681472 chr11:10681465-10681472 chr11:10681464-10681473 chr11:10679139-10679149 chr11:10681440-10681448 chr11:10679138-10679150
18	NFIC	chr11:10678496-10679771	GM12878	blood:	n/a	n/a
19	RCOR1	chr11:10678669-10679206	K562	blood:	n/a	n/a
20	YY1	chr11:10678750-10679700	GM12892	blood:	n/a	chr11:10678919-10678941
21	ZNF143	chr11:10678702-10679203	K562	blood:	n/a	n/a
22	POLR2A	chr11:10678775-10679827	GM12892	blood:	n/a	n/a
23	SP1	chr11:10678730-10680078	HCT-116	colon:	n/a	n/a
24	RCOR1	chr11:10678769-10679357	K562	blood:	n/a	n/a
25	YY1	chr11:10678708-10679182	GM12878	blood:	n/a	chr11:10678919-10678941
26	TEAD4	chr11:10678768-10679434	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:10665821..10668759-chr11:10676865..10679050,3	K562	blood:
2	chr11:10675148..10677906-chr11:10678421..10681418,4	MCF-7	breast:
3	chr11:10678525..10679388-chr11:10716241..10717042,2	K562	blood:

Variant related genes	Relation type
MRVI1	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10770129	0.84[JPT][hapmap]
rs10770130	0.90[ASN][1000 genomes]
rs10770132	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10770133	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840456	0.84[JPT][hapmap]
rs10840458	0.86[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10840459	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840460	0.88[ASN][1000 genomes]
rs10840461	0.88[ASN][1000 genomes]
rs10840462	0.88[ASN][1000 genomes]
rs10840463	0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10840464	0.88[ASN][1000 genomes]
rs10840465	0.88[ASN][1000 genomes]
rs10840466	0.88[ASN][1000 genomes]
rs10840467	0.87[ASN][1000 genomes]
rs10840468	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042910	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042913	0.88[ASN][1000 genomes]
rs12363422	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12420672	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12420675	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1390572	0.88[ASN][1000 genomes]
rs1390573	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1425149	0.88[ASN][1000 genomes]
rs1425150	0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1425151	0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1544862	0.88[ASN][1000 genomes]
rs1544863	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs16908157	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16908159	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16908162	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1845832	0.88[ASN][1000 genomes]
rs1874444	0.88[ASN][1000 genomes]
rs1895712	0.88[ASN][1000 genomes]
rs2098840	0.89[ASN][1000 genomes]
rs34554801	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35040034	0.88[ASN][1000 genomes]
rs35165550	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4243916	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4909946	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910166	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs722274	0.88[ASN][1000 genomes]
rs745336	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs750540	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7925193	0.84[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7933525	0.88[ASN][1000 genomes]
rs7938027	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7939662	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7939686	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs881870	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs903825	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903826	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903827	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903828	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11042911	OR2AG1	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10646000-10679000	Weak transcription	Fetal Lung	lung
2	chr11:10646200-10679200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:10664200-10678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:10672000-10679200	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr11:10673000-10682200	Enhancers	Placenta	Placenta
6	chr11:10673400-10679200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr11:10673400-10682800	Enhancers	Ovary	ovary
8	chr11:10673800-10678800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:10673800-10679200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:10673800-10681400	Weak transcription	Pancreas	Pancrea
11	chr11:10674000-10681400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:10674200-10681800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr11:10674400-10681400	Enhancers	Fetal Muscle Leg	muscle
14	chr11:10674400-10681800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr11:10674600-10689600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:10674800-10678800	Enhancers	Rectal Smooth Muscle	rectum
17	chr11:10675000-10678800	Enhancers	K562	blood
18	chr11:10675200-10679000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:10675400-10678800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:10675600-10678800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:10675800-10678800	Weak transcription	Stomach Mucosa	stomach
22	chr11:10675800-10680000	Weak transcription	Brain Angular Gyrus	brain
23	chr11:10676000-10679200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:10676000-10683200	Enhancers	NHDF-Ad	bronchial
25	chr11:10676200-10678800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:10676400-10679400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:10676400-10683400	Genic enhancers	Fetal Stomach	stomach
28	chr11:10676600-10678800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr11:10676600-10679000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:10676600-10679200	Enhancers	NH-A	brain
31	chr11:10676600-10681600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:10676800-10678800	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:10676800-10679200	Weak transcription	Brain Substantia Nigra	brain
34	chr11:10676800-10679800	Enhancers	Fetal Intestine Large	intestine
35	chr11:10677000-10679200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr11:10677000-10681800	Enhancers	HSMMtube	muscle
37	chr11:10677000-10682200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:10677000-10683400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:10677200-10678800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:10677200-10678800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:10677200-10678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:10677200-10679200	Weak transcription	HMEC	breast
43	chr11:10677200-10682800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:10677400-10678800	Weak transcription	A549	lung
45	chr11:10677400-10679200	Weak transcription	Fetal Intestine Small	intestine
46	chr11:10677400-10679800	Enhancers	Fetal Muscle Trunk	muscle
47	chr11:10677400-10680600	Genic enhancers	NHLF	lung
48	chr11:10677400-10680800	Enhancers	Small Intestine	intestine
49	chr11:10677400-10682200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr11:10677400-10683000	Enhancers	Spleen	Spleen

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