Variant report

Variant	rs4150673
Chromosome Location	chr11:18383449-18383450
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10734259	0.91[EUR][1000 genomes]
rs10741741	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741742	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832917	0.86[EUR][1000 genomes]
rs10832921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024634	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1140047	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12286683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12293544	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1520884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2061164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2124374	0.91[EUR][1000 genomes]
rs3740711	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]
rs3802968	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3825025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150526	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4150550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[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];0.83[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];0.95[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];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150566	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150588	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150609	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[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];0.95[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];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4150650	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150653	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4757637	1.00[CHB][hapmap]
rs4757645	0.86[CEU][hapmap]
rs6486419	0.83[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	0.83[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9988866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4150673	GTF2H1	cis	Esophagus Muscularis	GTEx
rs4150673	ABCC8	cis	parietal	SCAN
rs4150673	GTF2H1	cis	cerebellum	SCAN
rs4150673	GTF2H1	cis	parietal	SCAN
rs4150673	HPS5	cis	cerebellum	SCAN
rs4150673	HPS5	cis	multi-tissue	Pritchard
rs4150673	LDHA	cis	parietal	SCAN
rs4150673	GTF2H1	cis	Stomach	GTEx
rs4150673	GTF2H1	cis	Esophagus Mucosa	GTEx
rs4150673	PIK3C2A	cis	cerebellum	SCAN
rs4150673	NELL1	cis	parietal	SCAN
rs4150673	GTF2H1	cis	multi-tissue	Pritchard
rs4150673	GTF2H1	cis	lymphoblastoid	seeQTL
rs4150673	LDHAL6A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:18351200-18387000	Weak transcription	Stomach Mucosa	stomach
5	chr11:18352400-18389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:18354400-18389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:18357000-18389200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:18361800-18391600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:18363000-18390200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:18363200-18393000	Weak transcription	Fetal Heart	heart
11	chr11:18367600-18390000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:18369600-18385800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:18372800-18387200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr11:18373200-18386000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:18373200-18388200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:18373200-18389200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:18373200-18389200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:18373200-18389200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:18373200-18390600	Strong transcription	Adipose Nuclei	Adipose
20	chr11:18373400-18385600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:18373400-18388200	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr11:18373400-18389200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr11:18373400-18390000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:18373400-18390400	Strong transcription	Dnd41	blood
25	chr11:18373600-18389200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr11:18373600-18389800	Strong transcription	Liver	Liver
27	chr11:18373600-18389800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr11:18373600-18390200	Strong transcription	Fetal Thymus	thymus
29	chr11:18373600-18390400	Strong transcription	Placenta	Placenta
30	chr11:18373600-18391200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:18373800-18384000	Strong transcription	Primary T cells from cord blood	blood
32	chr11:18373800-18387200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:18373800-18387600	Strong transcription	Ovary	ovary
34	chr11:18373800-18388000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr11:18373800-18389200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr11:18373800-18389200	Strong transcription	Fetal Intestine Large	intestine
37	chr11:18373800-18389200	Strong transcription	Thymus	Thymus
38	chr11:18373800-18389400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:18373800-18389400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:18373800-18390400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:18374200-18386600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:18374400-18388800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:18374400-18388800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:18374400-18389000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:18374400-18389200	Strong transcription	Left Ventricle	heart
46	chr11:18374400-18389400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:18374400-18389400	Strong transcription	Fetal Intestine Small	intestine
48	chr11:18374600-18383800	Strong transcription	Brain Germinal Matrix	brain
49	chr11:18374600-18388800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:18374800-18389800	Strong transcription	Fetal Muscle Leg	muscle

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