Variant report

Variant	rs12225041
Chromosome Location	chr11:17333377-17333378
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10219196	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10466382	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766383	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10766384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10766385	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766387	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766389	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10832757	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832758	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832759	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832760	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832762	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832763	0.97[ASN][1000 genomes]
rs10832764	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832765	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832768	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832769	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832770	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10832771	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10832772	0.84[ASN][1000 genomes]
rs10832774	0.83[ASN][1000 genomes]
rs10832775	0.83[ASN][1000 genomes]
rs11024244	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024251	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024253	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024254	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024256	0.97[ASN][1000 genomes]
rs11024260	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024263	0.81[ASN][1000 genomes]
rs11525338	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2354867	0.83[ASN][1000 genomes]
rs4582955	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67904954	0.97[ASN][1000 genomes]
rs7950330	0.80[ASN][1000 genomes]
rs9645621	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1836937	chr11:17291499-17339127	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv1799284	chr11:17299390-17343486	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1799280	chr11:17299390-17354775	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv1801731	chr11:17299390-17354775	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv897017	chr11:17318236-17343486	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1843677	chr11:17327038-17337413	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv553582	chr11:17327038-17337413	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1841973	chr11:17327038-17339127	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1851915	chr11:17327038-17343486	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12225041	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs12225041	NCR3LG1	cis	Esophagus Mucosa	GTEx
rs12225041	KCNJ11	cis	Esophagus Mucosa	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17299000-17357200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:17299000-17357600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:17299000-17360600	Weak transcription	Small Intestine	intestine
4	chr11:17299200-17357000	Weak transcription	Brain Substantia Nigra	brain
5	chr11:17299400-17338200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:17299400-17355400	Weak transcription	Brain Angular Gyrus	brain
7	chr11:17299400-17357000	Weak transcription	Fetal Intestine Large	intestine
8	chr11:17299600-17335000	Weak transcription	Primary B cells from cord blood	blood
9	chr11:17300200-17335000	Weak transcription	Fetal Brain Male	brain
10	chr11:17301600-17350400	Weak transcription	Fetal Heart	heart
11	chr11:17306200-17353000	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:17307800-17333600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:17308200-17335800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:17308200-17353600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:17308200-17357600	Weak transcription	HepG2	liver
16	chr11:17308200-17360800	Strong transcription	Fetal Thymus	thymus
17	chr11:17308200-17372600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:17308400-17335000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:17308400-17335000	Weak transcription	NHLF	lung
20	chr11:17308400-17356800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:17308400-17361600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:17309000-17355600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:17309400-17335200	Weak transcription	Psoas Muscle	Psoas
24	chr11:17312200-17355400	Weak transcription	Fetal Kidney	kidney
25	chr11:17313800-17335400	Weak transcription	HSMMtube	muscle
26	chr11:17314200-17353400	Weak transcription	Stomach Mucosa	stomach
27	chr11:17314400-17335000	Strong transcription	Dnd41	blood
28	chr11:17315200-17335000	Weak transcription	Colonic Mucosa	Colon
29	chr11:17315400-17335000	Weak transcription	Spleen	Spleen
30	chr11:17315400-17353400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:17316000-17335200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr11:17316000-17360000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:17316000-17361000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:17316400-17347600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:17316600-17349800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:17318400-17355600	Weak transcription	Gastric	stomach
37	chr11:17318600-17350400	Weak transcription	Right Ventricle	heart
38	chr11:17318600-17353600	Weak transcription	Brain Anterior Caudate	brain
39	chr11:17318800-17334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:17319000-17335200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:17319000-17336600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr11:17319000-17356400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:17319400-17334600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:17320200-17349800	Weak transcription	Esophagus	oesophagus
45	chr11:17320600-17334600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:17320600-17349800	Weak transcription	Fetal Intestine Small	intestine
47	chr11:17320800-17372400	Weak transcription	GM12878-XiMat	blood
48	chr11:17322000-17335200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr11:17322600-17356200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:17323000-17337000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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