Variant report

Variant	rs11024634
Chromosome Location	chr11:18392074-18392075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18389829..18393207-chr11:18415267..18417660,3	K562	blood:
2	chr11:18386073..18387800-chr11:18389640..18392386,2	K562	blood:
3	chr11:18390732..18392479-chr11:18415393..18418299,2	MCF-7	breast:
4	chr11:18389913..18393253-chr11:18414767..18417568,3	K562	blood:

Variant related genes	Relation type
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10734259	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10741741	0.83[EUR][1000 genomes]
rs10741742	0.91[EUR][1000 genomes]
rs10832917	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10832921	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1140047	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12286683	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12293544	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1520884	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2061164	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2124374	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3740711	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3802968	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3825025	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150526	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150550	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150561	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150562	0.94[EUR][1000 genomes]
rs4150564	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150566	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150575	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150579	0.95[EUR][1000 genomes]
rs4150588	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4150609	0.94[EUR][1000 genomes]
rs4150610	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150612	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4150615	0.97[EUR][1000 genomes]
rs4150616	0.97[EUR][1000 genomes]
rs4150622	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4150641	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4150650	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150651	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150653	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150655	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4150661	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150673	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4353250	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6486419	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7103375	0.87[ASN][1000 genomes]
rs7129995	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7947378	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9783347	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9988866	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv523373	chr11:18382911-18401531	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv1811183	chr11:18389643-18432437	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11024634	GTF2H1	cis	Stomach	GTEx
rs11024634	GTF2H1	cis	Esophagus Mucosa	GTEx
rs11024634	GTF2H1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:18363200-18393000	Weak transcription	Fetal Heart	heart
3	chr11:18385000-18392600	Weak transcription	Small Intestine	intestine
4	chr11:18387600-18393200	Weak transcription	Gastric	stomach
5	chr11:18387600-18394000	Weak transcription	Fetal Stomach	stomach
6	chr11:18387600-18395400	Weak transcription	Lung	lung
7	chr11:18387600-18398600	Weak transcription	Ovary	ovary
8	chr11:18387600-18404200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:18387600-18404400	Weak transcription	Esophagus	oesophagus
10	chr11:18387600-18404800	Weak transcription	Pancreas	Pancrea
11	chr11:18387800-18404400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:18388000-18405000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:18388200-18392600	Weak transcription	Stomach Mucosa	stomach
14	chr11:18388200-18392600	Weak transcription	K562	blood
15	chr11:18388200-18393400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr11:18388200-18395000	Weak transcription	NHLF	lung
17	chr11:18388400-18402600	Weak transcription	Hela-S3	cervix
18	chr11:18388600-18392800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:18388600-18394400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:18388800-18393000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:18388800-18404400	Weak transcription	Brain Anterior Caudate	brain
22	chr11:18389000-18393000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr11:18389000-18393400	Weak transcription	Brain Germinal Matrix	brain
24	chr11:18389200-18392400	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:18389200-18392600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr11:18389200-18392600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr11:18389200-18392600	Weak transcription	Left Ventricle	heart
28	chr11:18389200-18392800	Weak transcription	HepG2	liver
29	chr11:18389200-18393000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr11:18389200-18394400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr11:18389200-18404600	Weak transcription	Thymus	Thymus
32	chr11:18389400-18392400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:18389400-18392400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:18389400-18394600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:18389400-18394800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:18389800-18392400	Weak transcription	Liver	Liver
37	chr11:18389800-18392600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr11:18389800-18393000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr11:18390000-18392400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:18390000-18392600	Weak transcription	Fetal Intestine Large	intestine
41	chr11:18390000-18393000	Strong transcription	Primary T cells from cord blood	blood
42	chr11:18390000-18393000	Weak transcription	Brain Substantia Nigra	brain
43	chr11:18390000-18394200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:18390000-18404400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:18390000-18404400	Weak transcription	Fetal Brain Female	brain
46	chr11:18390200-18393000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:18390200-18393200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:18390200-18394200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:18390200-18404200	Weak transcription	Fetal Thymus	thymus
50	chr11:18390400-18393000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links