Variant report

Variant	rs2441990
Chromosome Location	chr9:17496975-17496976
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1022715	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1885168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1885169	1.00[JPT][hapmap]
rs2145661	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2145664	1.00[JPT][hapmap]
rs2180903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2208504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2208505	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2224456	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2248131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2441988	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441989	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442006	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2499056	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2499060	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2593349	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2593351	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593391	0.88[EUR][1000 genomes]
rs2754312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2754313	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs2754314	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2754319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2754323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2754339	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2754340	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv892668	chr9:17371690-17532840	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892670	chr9:17378776-17507277	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv892671	chr9:17378776-17610211	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv2422265	chr9:17396711-17598187	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv973451	chr9:17493434-17498572	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2441990	PSMD2	trans	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17448000-17503400	Weak transcription	Ovary	ovary
2	chr9:17453000-17497000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:17453800-17504200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:17455600-17503000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:17458800-17500400	Weak transcription	HUVEC	blood vessel
6	chr9:17468200-17497200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:17468200-17500000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:17468200-17500200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr9:17477000-17497000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:17482000-17497400	Weak transcription	Fetal Stomach	stomach
11	chr9:17482000-17499000	Weak transcription	Aorta	Aorta
12	chr9:17483600-17497800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:17484600-17499000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:17486600-17500000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:17487800-17498200	Weak transcription	Adipose Nuclei	Adipose
16	chr9:17489600-17497600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:17492800-17506400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:17495800-17497200	Strong transcription	Fetal Lung	lung
19	chr9:17495800-17497800	Strong transcription	Liver	Liver
20	chr9:17496200-17502800	Weak transcription	Left Ventricle	heart
21	chr9:17496400-17499200	Weak transcription	Dnd41	blood
22	chr9:17496400-17502800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr9:17496400-17503000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:17496600-17498200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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