Variant report

Variant	rs4554574
Chromosome Location	chr9:17379849-17379850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10115784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1023778	0.82[YRI][hapmap]
rs10738475	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10756862	0.82[AFR][1000 genomes]
rs10756864	0.82[AFR][1000 genomes]
rs10756879	0.84[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs10962922	0.80[JPT][hapmap]
rs10962924	0.81[JPT][hapmap]
rs10962939	0.81[JPT][hapmap]
rs10962941	0.85[YRI][hapmap]
rs10962957	0.96[EUR][1000 genomes]
rs10962978	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10962979	0.81[AFR][1000 genomes]
rs10962995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10963070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10963103	0.91[CEU][hapmap]
rs10963105	1.00[CEU][hapmap]
rs1113379	0.81[JPT][hapmap]
rs1113380	0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1113381	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12164282	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12235811	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12236166	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12236896	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12237062	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12238680	0.92[EUR][1000 genomes]
rs12346397	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1348279	0.86[AFR][1000 genomes]
rs1372704	1.00[CEU][hapmap]
rs1413418	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs1413419	0.81[JPT][hapmap]
rs1576958	0.81[JPT][hapmap]
rs1582029	0.81[JPT][hapmap]
rs1583985	1.00[CEU][hapmap]
rs16935416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs1759452	0.80[JPT][hapmap]
rs1759453	0.81[JPT][hapmap]
rs1759457	1.00[YRI][hapmap]
rs1759458	0.81[JPT][hapmap]
rs1759459	0.81[JPT][hapmap]
rs1759460	0.81[JPT][hapmap]
rs1759462	0.81[JPT][hapmap]
rs1759463	0.81[JPT][hapmap]
rs1759464	0.95[YRI][hapmap]
rs1759615	0.86[ASN][1000 genomes]
rs1759616	0.81[JPT][hapmap]
rs1930639	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1930641	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2010086	0.92[AFR][1000 genomes]
rs2083694	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs2083695	0.91[AFR][1000 genomes]
rs2099859	0.91[AFR][1000 genomes]
rs2165688	0.90[AFR][1000 genomes]
rs2210551	0.88[AFR][1000 genomes]
rs2274916	0.91[CEU][hapmap]
rs2441991	1.00[CEU][hapmap]
rs2584539	1.00[CEU][hapmap]
rs2584548	1.00[CEU][hapmap]
rs2593389	0.81[YRI][hapmap]
rs2593397	1.00[CEU][hapmap]
rs2593418	1.00[CEU][hapmap]
rs2780203	1.00[CEU][hapmap]
rs2780204	0.81[JPT][hapmap]
rs2780205	0.81[JPT][hapmap]
rs2780213	1.00[CEU][hapmap]
rs2815173	0.81[JPT][hapmap]
rs3739489	0.91[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs3808782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3808785	0.81[JPT][hapmap]
rs3814137	0.81[JPT][hapmap]
rs3814139	0.81[JPT][hapmap]
rs3891457	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4097851	0.80[AFR][1000 genomes]
rs4147023	0.81[JPT][hapmap]
rs4289910	0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs4621917	0.81[JPT][hapmap]
rs4961534	0.81[JPT][hapmap]
rs4961551	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4961554	0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs55863214	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs585682	0.80[JPT][hapmap]
rs600041	0.81[JPT][hapmap]
rs600133	0.81[JPT][hapmap]
rs601960	1.00[YRI][hapmap]
rs613966	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs614412	0.81[JPT][hapmap]
rs614471	0.81[JPT][hapmap]
rs620280	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs632176	0.81[JPT][hapmap]
rs634383	0.81[JPT][hapmap]
rs634446	0.81[JPT][hapmap]
rs642582	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs646025	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs647013	0.81[JPT][hapmap]
rs6475122	0.81[JPT][hapmap]
rs6475123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6475125	0.81[JPT][hapmap]
rs6475126	0.85[ASN][1000 genomes]
rs6475129	0.81[JPT][hapmap]
rs6475140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs659637	0.83[ASN][1000 genomes]
rs664447	0.81[JPT][hapmap]
rs673587	0.81[JPT][hapmap]
rs7020918	0.81[JPT][hapmap]
rs7027539	0.81[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs7028582	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7034768	0.81[JPT][hapmap]
rs7035525	0.86[JPT][hapmap]
rs7037019	0.92[AFR][1000 genomes]
rs7042700	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7043703	0.81[JPT][hapmap]
rs7046327	0.81[JPT][hapmap]
rs7047093	0.81[JPT][hapmap];0.92[YRI][hapmap]
rs7862336	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7865807	0.81[JPT][hapmap];0.85[YRI][hapmap]
rs7870334	1.00[CEU][hapmap]
rs7874945	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs870270	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs9657595	0.92[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv466271	chr9:17329964-17438391	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv613696	chr9:17329964-17438391	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1015524	chr9:17350843-17419424	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	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
11	nsv892669	chr9:17378776-17438391	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	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
13	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4554574	PIP4K2B	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17362000-17394600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr9:17368400-17394600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:17368400-17457800	Weak transcription	Pancreas	Pancrea
4	chr9:17368600-17394800	Weak transcription	Adipose Nuclei	Adipose
5	chr9:17368600-17411200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:17368600-17411400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:17368600-17411400	Weak transcription	Aorta	Aorta
8	chr9:17368800-17380400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:17368800-17411400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:17369000-17380600	Weak transcription	Fetal Lung	lung
11	chr9:17369000-17395000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:17369200-17380000	Weak transcription	Left Ventricle	heart
13	chr9:17369200-17380200	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:17369400-17411200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr9:17370000-17380200	Weak transcription	Ovary	ovary
16	chr9:17370600-17386600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:17371400-17394800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:17371600-17380200	Weak transcription	Liver	Liver
19	chr9:17377600-17403000	Weak transcription	Fetal Stomach	stomach
20	chr9:17377800-17383800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:17379400-17381400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:17379400-17404200	Weak transcription	Psoas Muscle	Psoas
23	chr9:17379600-17394800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:17379800-17394600	Weak transcription	Monocytes-CD14+_RO01746	blood

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