Variant report

Variant	rs4150653
Chromosome Location	chr11:18374782-18374783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10734259	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10741741	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10741742	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10832917	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10832921	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024634	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1140047	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12286683	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12293544	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1520884	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2061164	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2124374	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3740711	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3802968	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3825025	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150526	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150550	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150561	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150562	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150564	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150566	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150575	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150579	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4150588	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150609	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150610	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150612	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150615	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4150616	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4150622	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150641	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150642	0.87[ASN][1000 genomes]
rs4150650	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150651	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150655	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150661	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150673	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4353250	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6486419	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7103375	1.00[ASN][1000 genomes]
rs7129995	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7947378	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9783347	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9988866	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4150653	GTF2H1	cis	Esophagus Muscularis	GTEx
rs4150653	GTF2H1	cis	Stomach	GTEx
rs4150653	GTF2H1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:18346800-18382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:18351200-18387000	Weak transcription	Stomach Mucosa	stomach
7	chr11:18352400-18389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:18354400-18389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:18357000-18389200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:18357200-18379600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:18360000-18382200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:18361800-18391600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:18363000-18390200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:18363200-18379400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:18363200-18393000	Weak transcription	Fetal Heart	heart
16	chr11:18365800-18381400	Weak transcription	Pancreas	Pancrea
17	chr11:18366600-18381400	Weak transcription	Gastric	stomach
18	chr11:18367200-18375400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr11:18367600-18390000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:18368000-18376000	Weak transcription	Right Ventricle	heart
21	chr11:18368000-18382400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:18368200-18375400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:18368200-18379400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:18368200-18379800	Weak transcription	Fetal Brain Male	brain
25	chr11:18368600-18381400	Weak transcription	Spleen	Spleen
26	chr11:18369600-18374800	Weak transcription	Esophagus	oesophagus
27	chr11:18369600-18379600	Weak transcription	Colon Smooth Muscle	Colon
28	chr11:18369600-18385800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:18369800-18377000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:18369800-18379600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:18369800-18380600	Weak transcription	NHLF	lung
32	chr11:18370000-18374800	Weak transcription	Brain Anterior Caudate	brain
33	chr11:18370000-18375000	Weak transcription	GM12878-XiMat	blood
34	chr11:18370000-18377400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:18370000-18378600	Weak transcription	HepG2	liver
36	chr11:18370000-18379200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:18370000-18379200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr11:18370200-18374800	Weak transcription	Colonic Mucosa	Colon
39	chr11:18370200-18379800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:18370400-18374800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:18370400-18377400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:18370400-18380000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr11:18370600-18375000	Weak transcription	Brain Angular Gyrus	brain
44	chr11:18370600-18375200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr11:18370600-18379800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr11:18371200-18377200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr11:18371400-18376000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:18371400-18376400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:18371400-18377200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr11:18371800-18374800	Weak transcription	Fetal Muscle Leg	muscle

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