Variant report

Variant	rs13060048
Chromosome Location	chr3:52598608-52598609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 171 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs10433615	0.80[ASN][1000 genomes]
rs10510760	0.85[ASN][1000 genomes]
rs10865974	0.80[EUR][1000 genomes]
rs11130307	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130308	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130310	0.82[EUR][1000 genomes]
rs11130311	0.83[ASN][1000 genomes]
rs11130312	0.85[ASN][1000 genomes]
rs11130313	0.85[ASN][1000 genomes]
rs11130314	0.83[ASN][1000 genomes]
rs11130315	0.83[ASN][1000 genomes]
rs1133415	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708075	0.88[ASN][1000 genomes]
rs11709284	0.90[ASN][1000 genomes]
rs11709448	0.85[ASN][1000 genomes]
rs11711421	0.87[ASN][1000 genomes]
rs11714030	0.81[EUR][1000 genomes]
rs11714419	0.84[ASN][1000 genomes]
rs11714565	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11716747	0.82[EUR][1000 genomes]
rs11717043	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11718420	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11718509	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11719514	0.81[ASN][1000 genomes]
rs11720159	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11720243	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720432	0.85[ASN][1000 genomes]
rs12486847	0.83[ASN][1000 genomes]
rs12487445	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487591	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12488461	0.81[ASN][1000 genomes]
rs12489732	0.95[ASN][1000 genomes]
rs12489828	0.89[ASN][1000 genomes]
rs12498066	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12629699	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12629701	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12632265	0.81[ASN][1000 genomes]
rs12632381	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12635140	0.80[EUR][1000 genomes]
rs13059862	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060675	0.84[ASN][1000 genomes]
rs13063160	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064064	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13065019	0.85[ASN][1000 genomes]
rs13065851	0.85[ASN][1000 genomes]
rs13068293	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13069481	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13076398	0.97[ASN][1000 genomes]
rs13079063	0.82[EUR][1000 genomes]
rs13081031	0.85[ASN][1000 genomes]
rs13085331	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13085775	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13085895	0.85[ASN][1000 genomes]
rs13086297	0.85[ASN][1000 genomes]
rs13086898	0.83[ASN][1000 genomes]
rs13303	0.89[ASN][1000 genomes]
rs13621	0.95[ASN][1000 genomes]
rs1468638	0.82[EUR][1000 genomes]
rs1561337	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17052256	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17052259	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17264436	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1821879	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1866268	0.80[EUR][1000 genomes]
rs1961958	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961959	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028216	0.83[ASN][1000 genomes]
rs2079929	0.81[EUR][1000 genomes]
rs2083180	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109634	0.82[EUR][1000 genomes]
rs2118540	0.85[ASN][1000 genomes]
rs2164884	0.86[ASN][1000 genomes]
rs2251219	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289247	0.80[EUR][1000 genomes]
rs2289249	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289250	0.85[ASN][1000 genomes]
rs2336145	0.85[ASN][1000 genomes]
rs2336146	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2336148	0.80[ASN][1000 genomes]
rs2336149	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2590838	0.81[ASN][1000 genomes]
rs2590846	0.83[ASN][1000 genomes]
rs28661185	0.89[ASN][1000 genomes]
rs2878628	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33964154	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33967311	0.85[ASN][1000 genomes]
rs34005367	0.94[ASN][1000 genomes]
rs34115864	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34173654	0.86[ASN][1000 genomes]
rs34215106	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34341238	0.83[ASN][1000 genomes]
rs34537256	0.85[ASN][1000 genomes]
rs34610142	0.81[ASN][1000 genomes]
rs34739010	0.81[EUR][1000 genomes]
rs34754793	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34757451	0.85[ASN][1000 genomes]
rs34954168	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35107891	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35211965	0.85[ASN][1000 genomes]
rs35249778	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35409678	0.83[ASN][1000 genomes]
rs35526119	0.82[EUR][1000 genomes]
rs35976524	0.83[ASN][1000 genomes]
rs3733041	0.80[EUR][1000 genomes]
rs3733045	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755798	0.80[EUR][1000 genomes]
rs3755806	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774365	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774366	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796353	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3852066	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4234633	0.89[ASN][1000 genomes]
rs4282054	0.89[ASN][1000 genomes]
rs4434138	0.89[ASN][1000 genomes]
rs4475032	0.94[ASN][1000 genomes]
rs4687546	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687547	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687548	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687624	0.89[ASN][1000 genomes]
rs4687625	0.94[ASN][1000 genomes]
rs4687626	0.95[ASN][1000 genomes]
rs4687629	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687630	0.84[ASN][1000 genomes]
rs4687633	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687636	0.85[ASN][1000 genomes]
rs4687637	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687638	0.85[ASN][1000 genomes]
rs4687639	0.86[ASN][1000 genomes]
rs4687644	0.82[EUR][1000 genomes]
rs62253700	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62253703	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62253733	0.85[ASN][1000 genomes]
rs62255362	0.83[ASN][1000 genomes]
rs62256903	0.97[ASN][1000 genomes]
rs6445528	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445529	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445534	0.80[EUR][1000 genomes]
rs6762457	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6768697	0.83[ASN][1000 genomes]
rs6770463	0.83[ASN][1000 genomes]
rs6778735	0.87[ASN][1000 genomes]
rs6778844	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6786043	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786919	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788887	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788993	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790330	0.85[ASN][1000 genomes]
rs6796726	0.84[ASN][1000 genomes]
rs6798246	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68021750	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6803012	0.81[ASN][1000 genomes]
rs6804145	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6805156	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7611731	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614498	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7614981	0.89[ASN][1000 genomes]
rs7622694	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7623199	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7624716	0.82[EUR][1000 genomes]
rs7625743	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628578	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7636227	0.89[ASN][1000 genomes]
rs7638808	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7642198	0.82[ASN][1000 genomes]
rs7652191	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs767418	0.81[EUR][1000 genomes]
rs9758945	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9917834	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv822092	chr3:52598226-52601851	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13060048	PBRM1	cis	Artery Tibial	GTEx
rs13060048	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs13060048	PBRM1	cis	Thyroid	GTEx
rs13060048	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs13060048	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:52574400-52623800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:52574600-52598800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:52574800-52605000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:52576800-52625600	Strong transcription	Fetal Thymus	thymus
6	chr3:52577000-52599000	Strong transcription	Fetal Muscle Leg	muscle
7	chr3:52577200-52599000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:52577600-52605200	Strong transcription	Dnd41	blood
9	chr3:52578200-52625600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:52578400-52600600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:52578800-52598800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:52578800-52599600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:52578800-52601400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:52579000-52599200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:52580800-52598800	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:52581000-52601000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:52583200-52600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:52583200-52600800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:52584600-52599000	Strong transcription	Primary hematopoietic stem cells	blood
20	chr3:52585800-52627400	Weak transcription	Fetal Heart	heart
21	chr3:52587000-52602400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:52587600-52599200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:52587800-52598800	Strong transcription	Brain Germinal Matrix	brain
25	chr3:52589400-52599000	Strong transcription	Liver	Liver
26	chr3:52589600-52611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:52591200-52599000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:52591200-52601400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:52591400-52598800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:52591400-52599200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:52591400-52599200	Strong transcription	Fetal Intestine Large	intestine
33	chr3:52591600-52598800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:52592400-52599000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:52592400-52601600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:52592600-52607600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:52592600-52610400	Weak transcription	A549	lung
39	chr3:52594200-52598800	Strong transcription	Colon Smooth Muscle	Colon
40	chr3:52594400-52607800	Weak transcription	Aorta	Aorta
41	chr3:52594400-52614800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:52595200-52599600	Strong transcription	Fetal Intestine Small	intestine
43	chr3:52595200-52631000	Weak transcription	Stomach Mucosa	stomach
44	chr3:52595400-52599600	Strong transcription	Fetal Stomach	stomach
45	chr3:52595800-52598800	Strong transcription	NHDF-Ad	bronchial
46	chr3:52595800-52599000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:52595800-52607800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:52596000-52599400	Weak transcription	Hela-S3	cervix
49	chr3:52596000-52600000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:52596000-52600800	Strong transcription	Osteobl	bone

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