Variant report

Variant	rs7120394
Chromosome Location	chr11:74034473-74034474
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPME1-1	chr11:74033752-74035048	ENSG00000246211

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1044782	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1053021	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs10736795	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10793072	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10793073	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10793074	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10793075	0.83[ASN][1000 genomes]
rs10793079	0.83[JPT][hapmap]
rs10793080	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10793081	0.85[CHB][hapmap];0.82[MEX][hapmap]
rs11236061	0.83[ASN][1000 genomes]
rs11236087	0.82[MEX][hapmap]
rs11236088	0.82[MEX][hapmap]
rs12146503	0.81[EUR][1000 genomes]
rs2887119	0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs3168173	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3741130	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs3862799	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3867268	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3867270	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs3867271	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs3867272	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs479968	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs480358	0.85[CHB][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap]
rs486758	0.85[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4944041	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944887	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519083	0.83[ASN][1000 genomes]
rs538103	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs563626	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58950228	0.84[ASN][1000 genomes]
rs592644	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs595798	0.83[ASN][1000 genomes]
rs596976	0.85[CHB][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs598869	0.85[CHB][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs623065	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs625632	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs634608	0.84[CHB][hapmap];0.84[TSI][hapmap];0.80[ASN][1000 genomes]
rs637921	0.83[ASN][1000 genomes]
rs641271	0.83[ASN][1000 genomes]
rs655719	0.85[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs662393	0.89[AMR][1000 genomes]
rs673103	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7926851	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7928036	0.83[ASN][1000 genomes]
rs7930193	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934621	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7940145	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7941916	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7944333	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7945908	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7947911	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv555425	chr11:74025055-74034473	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv555429	chr11:74025279-74034473	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7120394	FZD9	trans	brain	seeQTL
rs7120394	C2CD3	cis	parietal	SCAN
rs7120394	UCP2	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74023200-74036800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:74028800-74038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:74030200-74035400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:74030800-74036600	Weak transcription	HSMM	muscle
5	chr11:74030800-74037200	Weak transcription	Aorta	Aorta
6	chr11:74031200-74036200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:74031200-74071200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:74031400-74034600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:74031600-74034600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:74032000-74034600	Enhancers	Psoas Muscle	Psoas
11	chr11:74032800-74034600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:74032800-74034800	Enhancers	Adipose Nuclei	Adipose
13	chr11:74032800-74034800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr11:74033000-74036600	Weak transcription	Pancreas	Pancrea
15	chr11:74033000-74037000	Weak transcription	Right Ventricle	heart
16	chr11:74033000-74037000	Weak transcription	A549	lung
17	chr11:74033200-74036600	Weak transcription	Left Ventricle	heart
18	chr11:74033200-74047200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr11:74033400-74036400	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:74033600-74040600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:74034000-74035000	Weak transcription	Fetal Muscle Leg	muscle
22	chr11:74034000-74035400	Weak transcription	Fetal Brain Female	brain
23	chr11:74034000-74036200	Weak transcription	Fetal Brain Male	brain
24	chr11:74034000-74036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:74034000-74036600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:74034000-74036600	Weak transcription	Brain Germinal Matrix	brain
27	chr11:74034000-74036600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:74034000-74036600	Weak transcription	Ovary	ovary
29	chr11:74034000-74036600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:74034000-74036600	Weak transcription	NHLF	lung
31	chr11:74034000-74036800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:74034000-74036800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:74034000-74036800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:74034200-74036400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:74034200-74036400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:74034200-74036600	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:74034200-74036600	Weak transcription	Fetal Lung	lung
38	chr11:74034200-74036600	Weak transcription	NH-A	brain
39	chr11:74034200-74036800	Weak transcription	Lung	lung
40	chr11:74034200-74036800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:74034400-74035400	Weak transcription	HSMMtube	muscle
42	chr11:74034400-74036400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr11:74034400-74036400	Weak transcription	NHDF-Ad	bronchial
44	chr11:74034400-74036400	Weak transcription	Osteobl	bone
45	chr11:74034400-74036600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:74034400-74036600	Weak transcription	HUVEC	blood vessel

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