Variant report

Variant	rs2465653
Chromosome Location	chr11:120088728-120088729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120080610..120089931-chr11:120105398..120112199,18	K562	blood:
2	chr11:120087659..120092163-chr11:120106045..120111255,7	K562	blood:
3	chr11:120088424..120091961-chr11:120094010..120097522,6	K562	blood:
4	chr11:120082173..120084864-chr11:120088352..120091615,4	MCF-7	breast:
5	chr11:120040035..120042877-chr11:120088247..120091000,2	K562	blood:

Variant related genes	Relation type
ENSG00000137709	Chromatin interaction
ENSG00000184232	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10790371	0.81[EUR][1000 genomes]
rs1287394	0.88[ASN][1000 genomes]
rs2465654	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2847497	0.81[EUR][1000 genomes]
rs2953362	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477855	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499434	0.85[ASN][1000 genomes]
rs531698	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs537089	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs541857	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs576263	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs921574	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2465653	POU2F3	cis	Stomach	GTEx
rs2465653	POU2F3	cis	Nerve Tibial	GTEx
rs2465653	POU2F3	cis	Heart Left Ventricle	GTEx
rs2465653	POU2F3	cis	Adipose Subcutaneous	GTEx
rs2465653	POU2F3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120082800-120091800	Enhancers	Placenta	Placenta
2	chr11:120082800-120095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:120083600-120089000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:120083600-120089600	Weak transcription	Fetal Heart	heart
5	chr11:120083800-120094000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:120084000-120089000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:120084000-120092200	Weak transcription	Fetal Thymus	thymus
8	chr11:120084200-120093000	Genic enhancers	Fetal Muscle Leg	muscle
9	chr11:120084200-120102600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:120084400-120093000	Genic enhancers	Fetal Intestine Large	intestine
11	chr11:120084600-120089000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:120084600-120091400	Genic enhancers	Fetal Stomach	stomach
13	chr11:120084600-120091600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:120084600-120093200	Genic enhancers	Fetal Intestine Small	intestine
15	chr11:120084600-120095400	Weak transcription	Fetal Kidney	kidney
16	chr11:120084800-120092000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:120085000-120092800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr11:120085000-120093200	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr11:120085200-120092400	Enhancers	Ovary	ovary
20	chr11:120085800-120091000	Enhancers	Liver	Liver
21	chr11:120086000-120092800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr11:120086200-120090600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:120086200-120090800	Enhancers	Fetal Lung	lung
24	chr11:120086400-120090000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:120086400-120091600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
26	chr11:120086400-120092600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr11:120086400-120097000	Weak transcription	NHEK	skin
28	chr11:120086600-120088800	Genic enhancers	Colonic Mucosa	Colon
29	chr11:120086600-120095800	Weak transcription	NH-A	brain
30	chr11:120086800-120090200	Weak transcription	HSMM	muscle
31	chr11:120086800-120090600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:120087000-120090200	Weak transcription	NHDF-Ad	bronchial
33	chr11:120087200-120088800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:120087200-120089000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
35	chr11:120087200-120089800	Enhancers	Lung	lung
36	chr11:120087200-120093200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:120087400-120089200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:120087600-120090200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:120087600-120094000	Enhancers	Stomach Mucosa	stomach
40	chr11:120087800-120089000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:120087800-120089800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr11:120087800-120090000	Weak transcription	K562	blood
43	chr11:120088000-120090000	Weak transcription	Left Ventricle	heart
44	chr11:120088000-120092000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:120088200-120088800	Enhancers	Brain Hippocampus Middle	brain
46	chr11:120088200-120092600	Enhancers	Right Ventricle	heart
47	chr11:120088400-120089200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
48	chr11:120088400-120089200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr11:120088400-120089400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:120088400-120089400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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