Variant report

Variant	rs3740711
Chromosome Location	chr11:18379839-18379840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18378755..18381562-chr11:18416163..18418318,3	K562	blood:
2	chr11:18377382..18380490-chr11:18416157..18418987,3	K562	blood:
3	chr11:18350549..18352457-chr11:18378892..18380710,2	K562	blood:

Variant related genes	Relation type
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10734259	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10741741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741742	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832917	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10832921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024634	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1140047	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12286683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12293544	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1520884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2124374	0.91[EUR][1000 genomes]
rs3802968	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3825025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150526	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4150550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150566	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150588	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150609	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4150650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150653	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4757637	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4757645	0.86[CEU][hapmap]
rs6486419	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7103375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7129995	0.91[EUR][1000 genomes]
rs7947378	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9783347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9988866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][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
rs3740711	GTF2H1	cis	Esophagus Mucosa	GTEx
rs3740711	GTF2H1	cis	Stomach	GTEx
rs3740711	GTF2H1	cis	Esophagus Muscularis	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	chr11:18360000-18382200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:18361800-18391600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:18363000-18390200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:18363200-18393000	Weak transcription	Fetal Heart	heart
14	chr11:18365800-18381400	Weak transcription	Pancreas	Pancrea
15	chr11:18366600-18381400	Weak transcription	Gastric	stomach
16	chr11:18367600-18390000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:18368000-18382400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:18368600-18381400	Weak transcription	Spleen	Spleen
19	chr11:18369600-18385800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:18369800-18380600	Weak transcription	NHLF	lung
21	chr11:18370400-18380000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr11:18372800-18387200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr11:18373200-18386000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:18373200-18388200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:18373200-18389200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:18373200-18389200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:18373200-18389200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:18373200-18390600	Strong transcription	Adipose Nuclei	Adipose
29	chr11:18373400-18381800	Strong transcription	Primary B cells from cord blood	blood
30	chr11:18373400-18385600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:18373400-18388200	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr11:18373400-18389200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr11:18373400-18390000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:18373400-18390400	Strong transcription	Dnd41	blood
35	chr11:18373600-18389200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr11:18373600-18389800	Strong transcription	Liver	Liver
37	chr11:18373600-18389800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr11:18373600-18390200	Strong transcription	Fetal Thymus	thymus
39	chr11:18373600-18390400	Strong transcription	Placenta	Placenta
40	chr11:18373600-18391200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:18373800-18384000	Strong transcription	Primary T cells from cord blood	blood
42	chr11:18373800-18387200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:18373800-18387600	Strong transcription	Ovary	ovary
44	chr11:18373800-18388000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:18373800-18389200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr11:18373800-18389200	Strong transcription	Fetal Intestine Large	intestine
47	chr11:18373800-18389200	Strong transcription	Thymus	Thymus
48	chr11:18373800-18389400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:18373800-18389400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:18373800-18390400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links