Variant report

Variant	rs2780203
Chromosome Location	chr9:17432632-17432633
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 164 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10115784	1.00[CEU][hapmap]
rs10117379	0.92[ASN][1000 genomes]
rs10119233	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10119863	0.92[ASN][1000 genomes]
rs10119902	0.92[ASN][1000 genomes]
rs10120006	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10120013	0.92[ASN][1000 genomes]
rs10120733	0.94[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10120761	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10125886	0.92[ASN][1000 genomes]
rs1023778	0.88[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs10738477	0.92[ASN][1000 genomes]
rs10756879	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10810764	0.82[JPT][hapmap]
rs10810783	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10962922	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs10962924	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs10962939	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs10962995	1.00[CEU][hapmap]
rs10963056	1.00[CEU][hapmap]
rs10963067	1.00[CEU][hapmap]
rs10963070	1.00[CEU][hapmap]
rs10963081	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10963085	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10963088	0.94[ASN][1000 genomes]
rs10963103	0.91[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10963105	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1113379	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs1113380	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs12235811	0.92[CEU][hapmap]
rs1318162	0.87[JPT][hapmap]
rs1372698	0.85[ASW][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1372700	0.92[ASN][1000 genomes]
rs1372704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1413418	0.80[JPT][hapmap]
rs1413419	0.80[JPT][hapmap]
rs1442518	0.92[ASN][1000 genomes]
rs1442520	0.92[ASN][1000 genomes]
rs1442521	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1442522	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1442525	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1442526	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1576958	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs1582029	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs1583985	1.00[CEU][hapmap]
rs16935416	1.00[CEU][hapmap]
rs1759452	0.80[JPT][hapmap]
rs1759453	0.80[JPT][hapmap]
rs1759458	0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs1759459	0.80[JPT][hapmap]
rs1759460	0.80[JPT][hapmap]
rs1759462	0.80[JPT][hapmap]
rs1759463	0.80[JPT][hapmap]
rs1759465	0.81[CHD][hapmap]
rs1759616	0.80[JPT][hapmap]
rs1930639	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs1930641	0.81[CHD][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap]
rs1930647	0.88[ASN][1000 genomes]
rs1930648	0.92[ASN][1000 genomes]
rs2010086	0.82[ASN][1000 genomes]
rs2083694	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2119906	0.92[ASN][1000 genomes]
rs2119907	0.86[ASN][1000 genomes]
rs2274916	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2441991	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2584539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2584546	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2584548	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2584549	0.94[ASN][1000 genomes]
rs2584550	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2584551	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2584552	0.89[EUR][1000 genomes]
rs2593388	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2593389	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2593390	0.92[ASN][1000 genomes]
rs2593397	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2593416	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2780200	0.84[YRI][hapmap]
rs2780204	0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs2780205	0.80[JPT][hapmap]
rs2780208	0.90[ASN][1000 genomes]
rs2780210	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2780211	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2780213	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2780214	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3739488	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3739489	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3808781	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3808782	1.00[CEU][hapmap]
rs3808785	0.80[JPT][hapmap]
rs3814137	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs3814139	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs3891457	0.87[CHB][hapmap]
rs4147023	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs4554574	1.00[CEU][hapmap]
rs4621917	0.88[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs4961551	0.88[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap]
rs4961554	0.88[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs4961556	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs5001765	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600041	0.80[JPT][hapmap]
rs600133	0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs601960	0.81[CHD][hapmap];0.81[MEX][hapmap]
rs613966	0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs614412	0.80[JPT][hapmap]
rs614471	0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs620280	0.91[CEU][hapmap]
rs632176	0.80[JPT][hapmap]
rs634383	0.80[JPT][hapmap]
rs634446	0.80[JPT][hapmap]
rs642582	0.80[JPT][hapmap]
rs646025	0.81[CHD][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap]
rs647013	0.80[JPT][hapmap]
rs6475122	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs6475123	1.00[CEU][hapmap]
rs6475125	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs6475129	0.81[CHD][hapmap];0.80[JPT][hapmap]
rs6475140	1.00[CEU][hapmap]
rs664447	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs673587	0.80[JPT][hapmap]
rs679666	0.81[CHD][hapmap];0.81[MEX][hapmap]
rs7020918	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs7023305	0.92[ASN][1000 genomes]
rs7023540	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7026207	0.84[YRI][hapmap]
rs7027292	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7027539	0.88[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs7031133	0.81[JPT][hapmap]
rs7031361	1.00[CEU][hapmap]
rs7034768	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap]
rs7035276	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7035357	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7035525	0.82[CHB][hapmap]
rs7042700	0.87[CHB][hapmap]
rs7043703	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs7046327	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs7047093	0.82[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs7851688	0.84[YRI][hapmap]
rs7865807	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs7870334	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870427	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7872910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873708	0.82[JPT][hapmap]
rs7874945	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs870270	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs9298777	0.92[ASN][1000 genomes]
rs9298778	0.90[ASN][1000 genomes]
rs9657595	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
7	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
8	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
9	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
10	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
11	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
12	nsv466273	chr9:17391531-17436662	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv613697	chr9:17391531-17436662	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv523411	chr9:17394536-17454799	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2780203	PIP4K2B	trans	brain	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17368400-17457800	Weak transcription	Pancreas	Pancrea
2	chr9:17393400-17433000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr9:17396200-17440000	Weak transcription	Adipose Nuclei	Adipose
4	chr9:17408000-17437200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:17411800-17434400	Weak transcription	Dnd41	blood
6	chr9:17411800-17435600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:17411800-17439800	Weak transcription	Left Ventricle	heart
8	chr9:17411800-17481000	Weak transcription	Aorta	Aorta
9	chr9:17412200-17440200	Weak transcription	Fetal Stomach	stomach
10	chr9:17412200-17443600	Weak transcription	Ovary	ovary
11	chr9:17415800-17433600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:17417000-17433800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:17425400-17449600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:17426400-17466800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:17428000-17435800	Weak transcription	Liver	Liver
16	chr9:17428600-17440200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr9:17431000-17453400	Weak transcription	Fetal Lung	lung

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