Variant report

Variant	rs4150561
Chromosome Location	chr11:18354877-18354878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:18354865-18355160	HepG2	liver:	n/a	chr11:18355016-18355027
2	CEBPB	chr11:18354861-18355132	K562	blood:	n/a	chr11:18355016-18355027

No.	Distal block	Cell Line	Cell type
1	chr1:114636837..114637669-chr11:18354283..18354889,2	MCF-7	breast:
2	chr11:18354275..18358202-chr11:18415922..18417787,4	K562	blood:
3	chr11:18354275..18357110-chr11:18415922..18417548,3	K562	blood:
4	chr11:18342562..18345244-chr11:18353891..18356317,3	MCF-7	breast:

Variant related genes	Relation type
GTF2H1	TF binding region
ENSG00000110768	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000110756	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10734259	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741742	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832917	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10832921	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11024634	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1140047	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12291480	0.83[YRI][hapmap]
rs12293544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1520884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061163	0.82[AMR][1000 genomes]
rs2061164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124374	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3802968	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150526	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150566	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150588	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150609	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4150610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150642	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4150650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150653	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4353250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757637	1.00[CHB][hapmap]
rs4757645	0.86[CEU][hapmap]
rs6486419	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7103375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7129995	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947378	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9783347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9988866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4150561	GTF2H1	cis	Stomach	GTEx
rs4150561	GTF2H1	cis	Esophagus Mucosa	GTEx
rs4150561	GTF2H1	cis	Esophagus Muscularis	GTEx
rs4150561	GTF2H1	cis	multi-tissue	Pritchard

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	chr11:18346200-18355200	Weak transcription	Colonic Mucosa	Colon
4	chr11:18346400-18355200	Weak transcription	Gastric	stomach
5	chr11:18346400-18355200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:18346400-18357000	Weak transcription	Esophagus	oesophagus
7	chr11:18346400-18358400	Weak transcription	Right Ventricle	heart
8	chr11:18346400-18358600	Weak transcription	Fetal Brain Male	brain
9	chr11:18346600-18355200	Weak transcription	Fetal Kidney	kidney
10	chr11:18346600-18355200	Weak transcription	Ovary	ovary
11	chr11:18346800-18355000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:18346800-18355000	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:18346800-18355000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr11:18346800-18355200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:18346800-18372000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:18346800-18382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:18347000-18372400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr11:18347400-18366800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr11:18347400-18371200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:18347800-18368200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:18348000-18371200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:18348200-18355800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:18348400-18365800	Strong transcription	Osteobl	bone
26	chr11:18349400-18355000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:18349600-18357400	Weak transcription	Small Intestine	intestine
28	chr11:18350400-18355000	Weak transcription	Psoas Muscle	Psoas
29	chr11:18350400-18371200	Strong transcription	Dnd41	blood
30	chr11:18350400-18372000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:18350400-18372000	Strong transcription	Liver	Liver
32	chr11:18350600-18371600	Strong transcription	Fetal Intestine Large	intestine
33	chr11:18350800-18361800	Strong transcription	Lung	lung
34	chr11:18350800-18371200	Strong transcription	Fetal Thymus	thymus
35	chr11:18350800-18371800	Strong transcription	Fetal Muscle Leg	muscle
36	chr11:18350800-18372200	Strong transcription	Placenta	Placenta
37	chr11:18351000-18355000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:18351000-18368000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:18351200-18357000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:18351200-18357000	Weak transcription	Spleen	Spleen
41	chr11:18351200-18368200	Strong transcription	NH-A	brain
42	chr11:18351200-18373600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:18351200-18387000	Weak transcription	Stomach Mucosa	stomach
44	chr11:18351400-18355000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr11:18351600-18355000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr11:18351600-18362400	Weak transcription	Fetal Heart	heart
47	chr11:18351600-18368200	Strong transcription	NHEK	skin
48	chr11:18351600-18371200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:18351600-18371800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:18351800-18355000	Enhancers	Primary T cells fromperipheralblood	blood

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