Variant report

Variant	rs2465654
Chromosome Location	chr11:120099791-120099792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:120098962..120101044-chr11:120122301..120123827,2	K562	blood:
2	chr11:120099434..120101938-chr11:120172403..120174898,2	K562	blood:
3	chr11:120041545..120045663-chr11:120098074..120102653,6	MCF-7	breast:
4	chr11:120091006..120093784-chr11:120097633..120101741,5	K562	blood:
5	chr11:119993941..119995703-chr11:120098281..120100957,2	MCF-7	breast:
6	chr11:120099468..120100385-chr11:120173694..120174331,2	MCF-7	breast:
7	chr11:120099751..120100618-chr11:120170383..120171309,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM29-3	chr11:120099738-120101127	NONHSAT024720

No data

Variant related genes	Relation type
ENSG00000137699	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10790371	0.82[EUR][1000 genomes]
rs1295019	0.90[ASN][1000 genomes]
rs2465653	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2508489	0.87[ASN][1000 genomes]
rs2508490	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2847497	0.89[GIH][hapmap];0.82[EUR][1000 genomes]
rs2953362	0.98[EUR][1000 genomes]
rs3225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs472948	0.90[ASN][1000 genomes]
rs477855	0.92[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs505142	0.88[ASN][1000 genomes]
rs531698	0.97[EUR][1000 genomes]
rs537089	0.85[EUR][1000 genomes]
rs541857	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs576263	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs692804	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs921574	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9655	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];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
rs2465654	POU2F3	cis	Stomach	GTEx
rs2465654	POU2F3	cis	Esophagus Muscularis	GTEx
rs2465654	POU2F3	cis	Adipose Subcutaneous	GTEx
rs2465654	POU2F3	cis	Nerve Tibial	GTEx
rs2465654	POU2F3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120084200-120102600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:120091000-120102800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:120092800-120102000	Weak transcription	Brain Angular Gyrus	brain
4	chr11:120093600-120100600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:120094400-120100200	Strong transcription	HepG2	liver
6	chr11:120094800-120100800	Weak transcription	Stomach Mucosa	stomach
7	chr11:120095800-120100200	Strong transcription	Pancreas	Pancrea
8	chr11:120096000-120100600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr11:120096000-120100600	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:120096200-120100600	Weak transcription	Fetal Kidney	kidney
11	chr11:120096400-120101000	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr11:120096400-120101200	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr11:120096400-120102200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:120096600-120099800	Genic enhancers	Spleen	Spleen
15	chr11:120096600-120100200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:120096600-120100600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr11:120096600-120100800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:120096600-120110800	Weak transcription	Right Atrium	heart
19	chr11:120096800-120100000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:120096800-120100200	Weak transcription	Colon Smooth Muscle	Colon
21	chr11:120096800-120100400	Strong transcription	Colonic Mucosa	Colon
22	chr11:120096800-120101000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr11:120096800-120102400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:120097000-120099800	Strong transcription	Adipose Nuclei	Adipose
25	chr11:120097000-120100000	Weak transcription	Fetal Lung	lung
26	chr11:120097000-120100000	Strong transcription	Gastric	stomach
27	chr11:120097000-120101200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:120097000-120103000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:120097200-120100200	Strong transcription	Fetal Intestine Small	intestine
30	chr11:120097200-120101000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:120097200-120106200	Weak transcription	Esophagus	oesophagus
32	chr11:120097400-120100000	Strong transcription	Fetal Muscle Leg	muscle
33	chr11:120097400-120100400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr11:120097400-120100400	Strong transcription	NHLF	lung
35	chr11:120097400-120102000	Strong transcription	Fetal Intestine Large	intestine
36	chr11:120097600-120099800	Strong transcription	Ovary	ovary
37	chr11:120097600-120101600	Strong transcription	Liver	Liver
38	chr11:120097600-120102800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr11:120097800-120099800	Strong transcription	Fetal Stomach	stomach
40	chr11:120097800-120100200	Weak transcription	Brain Substantia Nigra	brain
41	chr11:120097800-120101000	Weak transcription	Brain Hippocampus Middle	brain
42	chr11:120097800-120102400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:120098200-120100400	Strong transcription	Placenta	Placenta
44	chr11:120098200-120102200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:120098200-120102400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr11:120098400-120100400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:120098400-120100800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:120098400-120101200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:120098600-120100600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:120098600-120101600	Weak transcription	Brain Anterior Caudate	brain

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