Variant report

Variant	rs71323391
Chromosome Location	chr3:48295700-48295701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 151 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1045482	0.84[EUR][1000 genomes]
rs11130162	0.84[EUR][1000 genomes]
rs11130163	0.84[EUR][1000 genomes]
rs11130164	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11706221	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11706277	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11707606	0.84[EUR][1000 genomes]
rs11707997	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11709691	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710257	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11710861	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714176	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11714944	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11715776	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715799	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11715876	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11716371	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11716848	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11717716	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11718329	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11718350	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11719365	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11928691	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13059037	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13060020	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13061269	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13066044	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13066758	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13067450	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13068265	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068288	0.81[EUR][1000 genomes]
rs13069029	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13070210	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13071960	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13072018	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13079728	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13081169	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13081633	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13082158	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13082859	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13084616	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13085251	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13087929	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13090538	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13094727	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13095983	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13097450	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13100815	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17647717	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17786132	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2125482	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2361685	0.84[EUR][1000 genomes]
rs2541	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3197223	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34076262	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34225441	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34523942	0.94[EUR][1000 genomes]
rs34589064	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34630841	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34728236	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34749846	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34946886	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35190747	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35297395	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35297486	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35411187	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35414021	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35456569	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35778847	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35802497	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35944878	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36020562	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36064160	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36075665	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36092070	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36121690	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3729577	0.84[EUR][1000 genomes]
rs3731487	0.84[EUR][1000 genomes]
rs3731489	0.84[EUR][1000 genomes]
rs3731497	0.84[EUR][1000 genomes]
rs3731513	0.84[EUR][1000 genomes]
rs3731515	0.84[EUR][1000 genomes]
rs3731534	0.83[EUR][1000 genomes]
rs3731550	0.84[EUR][1000 genomes]
rs3731555	0.84[EUR][1000 genomes]
rs3937	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4130522	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4131361	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131362	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4371540	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4392440	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4404473	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4420898	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4479622	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4511915	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4511916	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4541431	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4619808	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4632568	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6442110	0.84[EUR][1000 genomes]
rs6442111	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775179	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782166	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787500	0.84[EUR][1000 genomes]
rs6791930	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6793150	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6793223	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6793239	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6794644	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796343	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800492	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801801	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804986	0.92[EUR][1000 genomes]
rs6806112	0.82[EUR][1000 genomes]
rs71323394	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71323395	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71323396	0.90[EUR][1000 genomes]
rs71323397	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs745116	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7614532	0.94[EUR][1000 genomes]
rs7621785	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7624450	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7632297	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7636461	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7644414	0.85[EUR][1000 genomes]
rs7645425	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7647817	0.84[EUR][1000 genomes]
rs7648720	0.96[EUR][1000 genomes]
rs7652233	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7653152	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653336	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9311421	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936426	0.84[EUR][1000 genomes]
rs936427	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818937	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819094	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825637	0.92[EUR][1000 genomes]
rs9830016	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9831531	0.84[EUR][1000 genomes]
rs9833309	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834095	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9837228	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847953	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850672	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853804	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv3339173	chr3:48292529-48302277	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs71323391	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs71323391	ZNF589	cis	Esophagus Mucosa	GTEx
rs71323391	NME6	cis	Muscle Skeletal	GTEx
rs71323391	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs71323391	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs71323391	NME6	cis	Nerve Tibial	GTEx
rs71323391	MRPS18AP1	cis	Artery Aorta	GTEx
rs71323391	ZNF589	cis	Adipose Subcutaneous	GTEx
rs71323391	CDC25A	cis	Thyroid	GTEx
rs71323391	CDC25A	cis	Artery Tibial	GTEx
rs71323391	ZNF589	cis	Stomach	GTEx
rs71323391	MRPS18AP1	cis	lung	GTEx
rs71323391	NME6	cis	Artery Tibial	GTEx
rs71323391	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs71323391	ZNF589	cis	lung	GTEx
rs71323391	ZNF589	cis	Esophagus Muscularis	GTEx
rs71323391	CDC25A	cis	Muscle Skeletal	GTEx
rs71323391	ZNF589	cis	Nerve Tibial	GTEx
rs71323391	ZNF589	cis	Thyroid	GTEx
rs71323391	ZNF589	cis	Artery Tibial	GTEx
rs71323391	ZNF589	cis	Artery Aorta	GTEx
rs71323391	MRPS18AP1	cis	Stomach	GTEx
rs71323391	MRPS18AP1	cis	Thyroid	GTEx
rs71323391	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs71323391	MRPS18AP1	cis	Nerve Tibial	GTEx
rs71323391	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs71323391	FCF1P2	cis	Artery Tibial	GTEx
rs71323391	CDC25A	cis	Adipose Subcutaneous	GTEx
rs71323391	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs71323391	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs71323391	MRPS18AP1	cis	Artery Tibial	GTEx
rs71323391	SPINK8	cis	Whole Blood	GTEx
rs71323391	NME6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48283200-48309800	Weak transcription	Fetal Lung	lung
2	chr3:48283400-48297600	Weak transcription	Right Ventricle	heart
3	chr3:48283400-48300400	Weak transcription	Gastric	stomach
4	chr3:48283400-48310000	Weak transcription	NH-A	brain
5	chr3:48283400-48315200	Weak transcription	Ovary	ovary
6	chr3:48283600-48297800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:48283600-48300200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:48283600-48300800	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:48283600-48309600	Weak transcription	Fetal Intestine Large	intestine
10	chr3:48283800-48297600	Weak transcription	Esophagus	oesophagus
11	chr3:48283800-48307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:48283800-48309400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:48283800-48310400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:48284200-48297600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:48284200-48302800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:48285200-48297600	Weak transcription	Lung	lung
17	chr3:48285400-48303000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:48285600-48297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:48285600-48308200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:48285600-48312400	Weak transcription	Psoas Muscle	Psoas
21	chr3:48285800-48297600	Weak transcription	Aorta	Aorta
22	chr3:48285800-48300200	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:48285800-48307600	Weak transcription	Pancreas	Pancrea
24	chr3:48285800-48310200	Weak transcription	Fetal Brain Male	brain
25	chr3:48285800-48311000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:48286200-48295800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:48286400-48309400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:48287000-48297000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:48288400-48298200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:48288600-48312800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:48289200-48297400	Weak transcription	Brain Angular Gyrus	brain
32	chr3:48289200-48297800	Weak transcription	Primary B cells from cord blood	blood
33	chr3:48289200-48312000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:48289200-48312600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:48289600-48306800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:48289800-48307800	Weak transcription	Brain Anterior Caudate	brain
37	chr3:48290000-48295800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:48290000-48301400	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:48290000-48309400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:48290200-48297200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:48290200-48300200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:48290400-48297200	Weak transcription	HMEC	breast
43	chr3:48290400-48298000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:48290400-48298400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:48290400-48300400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:48290400-48300400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:48290400-48308200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:48290600-48296000	Weak transcription	HepG2	liver
49	chr3:48290600-48299000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:48290600-48299600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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