Variant report

Variant	rs11024254
Chromosome Location	chr11:17347455-17347456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10219196	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466382	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766383	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10766384	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10766385	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766387	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766389	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832757	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832758	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10832759	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832760	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832762	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832763	0.98[ASN][1000 genomes]
rs10832764	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832765	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832768	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832769	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832770	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832771	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10832772	0.85[ASN][1000 genomes]
rs10832773	0.81[ASN][1000 genomes]
rs10832774	0.84[ASN][1000 genomes]
rs10832775	0.84[ASN][1000 genomes]
rs11024244	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11024250	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024251	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024253	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024256	0.98[ASN][1000 genomes]
rs11024260	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024262	0.80[ASN][1000 genomes]
rs11024263	0.83[ASN][1000 genomes]
rs11525338	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225041	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2354867	0.85[ASN][1000 genomes]
rs4582955	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67904954	0.95[ASN][1000 genomes]
rs7950330	0.81[ASN][1000 genomes]
rs9645621	0.98[AMR][1000 genomes];0.95[EUR][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	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
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11024254	NCR3LG1	cis	Esophagus Mucosa	GTEx
rs11024254	KCNJ11	cis	Esophagus Mucosa	GTEx
rs11024254	RP1-239B22.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:102 , 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	chr11:17299400-17355400	Weak transcription	Brain Angular Gyrus	brain
6	chr11:17299400-17357000	Weak transcription	Fetal Intestine Large	intestine
7	chr11:17301600-17350400	Weak transcription	Fetal Heart	heart
8	chr11:17306200-17353000	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:17308200-17353600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:17308200-17357600	Weak transcription	HepG2	liver
11	chr11:17308200-17360800	Strong transcription	Fetal Thymus	thymus
12	chr11:17308200-17372600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:17308400-17356800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:17308400-17361600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:17309000-17355600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:17312200-17355400	Weak transcription	Fetal Kidney	kidney
17	chr11:17314200-17353400	Weak transcription	Stomach Mucosa	stomach
18	chr11:17315400-17353400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:17316000-17360000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:17316000-17361000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:17316400-17347600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:17316600-17349800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:17318400-17355600	Weak transcription	Gastric	stomach
24	chr11:17318600-17350400	Weak transcription	Right Ventricle	heart
25	chr11:17318600-17353600	Weak transcription	Brain Anterior Caudate	brain
26	chr11:17319000-17356400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:17320200-17349800	Weak transcription	Esophagus	oesophagus
28	chr11:17320600-17349800	Weak transcription	Fetal Intestine Small	intestine
29	chr11:17320800-17372400	Weak transcription	GM12878-XiMat	blood
30	chr11:17322600-17356200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:17324200-17353600	Weak transcription	Aorta	Aorta
32	chr11:17326400-17358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:17327600-17353800	Weak transcription	Ovary	ovary
34	chr11:17328200-17349800	Weak transcription	Pancreas	Pancrea
35	chr11:17328800-17349800	Weak transcription	Lung	lung
36	chr11:17330200-17358000	Weak transcription	K562	blood
37	chr11:17331800-17357400	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:17331800-17362000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:17333000-17349000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr11:17334000-17371000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:17335400-17355600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:17335400-17356000	Weak transcription	Colonic Mucosa	Colon
43	chr11:17335600-17348600	Weak transcription	Fetal Stomach	stomach
44	chr11:17335600-17361000	Strong transcription	Dnd41	blood
45	chr11:17335800-17353600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:17335800-17357200	Weak transcription	Fetal Brain Male	brain
47	chr11:17335800-17357600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr11:17336000-17349800	Weak transcription	Spleen	Spleen
49	chr11:17336000-17353800	Weak transcription	Primary B cells from cord blood	blood
50	chr11:17336000-17355000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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