Variant report

Variant	rs4150609
Chromosome Location	chr11:18364053-18364054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18363667..18365621-chr11:18424383..18427167,2	K562	blood:
2	chr11:18363292..18365134-chr11:18417577..18420472,2	K562	blood:
3	chr11:18363673..18366385-chr11:18369468..18372375,2	K562	blood:
4	chr11:18362164..18364564-chr11:18417285..18419232,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256006	Chromatin interaction
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10734259	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10741741	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10741742	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10832917	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10832921	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11024634	0.94[EUR][1000 genomes]
rs1140047	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12286683	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12293544	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1520884	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2061164	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2124374	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3740711	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3802968	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3825025	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150526	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4150550	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150561	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4150562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150564	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4150566	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150575	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150588	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150610	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150612	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150622	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150641	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150650	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150651	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150653	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150655	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150661	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150673	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4353250	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6486419	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7129995	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7947378	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9783347	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9988866	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[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
rs4150609	GTF2H1	cis	Stomach	GTEx
rs4150609	GTF2H1	cis	Esophagus Mucosa	GTEx
rs4150609	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	chr11:18346800-18372000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:18346800-18382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:18347000-18372400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:18347400-18366800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr11:18347400-18371200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr11:18347800-18368200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:18348000-18371200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:18348400-18365800	Strong transcription	Osteobl	bone
13	chr11:18350400-18371200	Strong transcription	Dnd41	blood
14	chr11:18350400-18372000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:18350400-18372000	Strong transcription	Liver	Liver
16	chr11:18350600-18371600	Strong transcription	Fetal Intestine Large	intestine
17	chr11:18350800-18371200	Strong transcription	Fetal Thymus	thymus
18	chr11:18350800-18371800	Strong transcription	Fetal Muscle Leg	muscle
19	chr11:18350800-18372200	Strong transcription	Placenta	Placenta
20	chr11:18351000-18368000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:18351200-18368200	Strong transcription	NH-A	brain
22	chr11:18351200-18373600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:18351200-18387000	Weak transcription	Stomach Mucosa	stomach
24	chr11:18351600-18368200	Strong transcription	NHEK	skin
25	chr11:18351600-18371200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:18351600-18371800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:18352000-18366000	Strong transcription	Fetal Brain Female	brain
28	chr11:18352000-18368400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:18352400-18371600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:18352400-18389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:18353200-18372200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:18353800-18366000	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr11:18353800-18368200	Strong transcription	Fetal Lung	lung
34	chr11:18353800-18368800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:18353800-18369600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr11:18353800-18372000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:18354000-18370600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:18354000-18371800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr11:18354000-18372200	Strong transcription	Adipose Nuclei	Adipose
40	chr11:18354200-18366800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:18354200-18368400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:18354200-18370600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:18354400-18370000	Strong transcription	Brain Anterior Caudate	brain
44	chr11:18354400-18371400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:18354400-18371600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:18354400-18371800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:18354400-18371800	Strong transcription	HSMM	muscle
48	chr11:18354400-18372000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr11:18354400-18389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr11:18354600-18365800	Strong transcription	Brain Cingulate Gyrus	brain

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