Variant report

Variant	rs12293544
Chromosome Location	chr11:18348581-18348582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18342879..18346241-chr11:18346771..18352447,12	MCF-7	breast:
2	chr11:18340646..18350403-chr11:18414573..18418572,22	K562	blood:
3	chr11:18347485..18350857-chr11:18414305..18419253,5	K562	blood:

Variant related genes	Relation type
ENSG00000134333	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000110768	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10734259	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741741	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10741742	0.88[AMR][1000 genomes];0.96[EUR][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	0.81[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];0.88[ASN][1000 genomes]
rs12286683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1520884	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061163	0.82[AMR][1000 genomes]
rs2061164	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2124374	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3740711	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];0.88[ASN][1000 genomes]
rs3825025	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150526	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150550	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4150561	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150562	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150564	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150566	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4150575	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150579	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150588	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150609	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150610	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150612	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150615	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150616	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150622	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150641	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150642	0.88[ASN][1000 genomes]
rs4150650	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150651	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150653	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150655	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150661	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150673	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4353250	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6486419	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7129995	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7947378	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9783347	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9988866	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	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
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12293544	GTF2H1	cis	Esophagus Mucosa	GTEx
rs12293544	GTF2H1	cis	Stomach	GTEx
rs12293544	GTF2H1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18344800-18349000	Weak transcription	Lung	lung
2	chr11:18344800-18353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:18345000-18353400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:18345000-18383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:18345200-18350800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:18345600-18350800	Weak transcription	Aorta	Aorta
8	chr11:18345800-18349400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:18346000-18349600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:18346200-18348600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:18346200-18349200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:18346200-18349400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:18346200-18351400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:18346200-18351400	Weak transcription	Right Atrium	heart
15	chr11:18346200-18352000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:18346200-18352600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:18346200-18355200	Weak transcription	Colonic Mucosa	Colon
18	chr11:18346400-18349000	Weak transcription	Thymus	Thymus
19	chr11:18346400-18349000	Weak transcription	Spleen	Spleen
20	chr11:18346400-18349400	Strong transcription	Psoas Muscle	Psoas
21	chr11:18346400-18350000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:18346400-18353000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:18346400-18353400	Weak transcription	Pancreas	Pancrea
24	chr11:18346400-18354600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:18346400-18355200	Weak transcription	Gastric	stomach
26	chr11:18346400-18355200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:18346400-18357000	Weak transcription	Esophagus	oesophagus
28	chr11:18346400-18358400	Weak transcription	Right Ventricle	heart
29	chr11:18346400-18358600	Weak transcription	Fetal Brain Male	brain
30	chr11:18346600-18349000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:18346600-18349200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr11:18346600-18349400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr11:18346600-18349400	Strong transcription	Placenta	Placenta
34	chr11:18346600-18349600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:18346600-18349800	Strong transcription	Fetal Thymus	thymus
36	chr11:18346600-18350400	Weak transcription	Stomach Mucosa	stomach
37	chr11:18346600-18350600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:18346600-18350600	Weak transcription	NH-A	brain
39	chr11:18346600-18350800	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:18346600-18351400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:18346600-18352200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr11:18346600-18353200	Weak transcription	Brain Germinal Matrix	brain
43	chr11:18346600-18355200	Weak transcription	Fetal Kidney	kidney
44	chr11:18346600-18355200	Weak transcription	Ovary	ovary
45	chr11:18346800-18349000	Weak transcription	HMEC	breast
46	chr11:18346800-18349400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr11:18346800-18349600	Strong transcription	Liver	Liver
48	chr11:18346800-18349800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:18346800-18350800	Weak transcription	Fetal Brain Female	brain
50	chr11:18346800-18350800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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