Variant report

Variant	rs4858876
Chromosome Location	chr3:48082861-48082862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1013431	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10446426	0.83[ASN][1000 genomes]
rs1060407	0.84[EUR][1000 genomes]
rs11130152	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130154	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130155	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1137524	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11707679	0.84[EUR][1000 genomes]
rs11710866	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11711129	0.86[EUR][1000 genomes]
rs11714518	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720151	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11924107	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12486714	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12493348	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13074973	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13075457	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075795	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13080997	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13081463	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13093830	0.84[EUR][1000 genomes]
rs1530646	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1550914	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1684942	0.82[ASN][1000 genomes]
rs184388	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2053767	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2121754	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2166770	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2166772	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2361683	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2361684	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631721	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28637561	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2882668	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319681	0.80[EUR][1000 genomes]
rs319682	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319684	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319685	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319686	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319689	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319690	0.82[EUR][1000 genomes]
rs319692	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319696	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34025851	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34597784	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34750113	0.84[EUR][1000 genomes]
rs35199727	0.84[EUR][1000 genomes]
rs35314534	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35689209	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3732529	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4293721	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4296617	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4392441	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4599334	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858871	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858880	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4858881	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4858882	0.86[EUR][1000 genomes]
rs4858887	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5012971	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56067795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60446735	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62260830	0.80[AMR][1000 genomes]
rs6442090	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6442091	0.95[EUR][1000 genomes]
rs6442094	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442096	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442099	0.80[EUR][1000 genomes]
rs6442101	0.91[EUR][1000 genomes]
rs6442102	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6766641	0.84[EUR][1000 genomes]
rs6768318	0.87[EUR][1000 genomes]
rs6770467	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6770477	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6772396	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6773208	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6777081	0.81[EUR][1000 genomes]
rs6783629	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6791834	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6803741	0.92[EUR][1000 genomes]
rs6806820	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7374482	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7374516	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7426976	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7427418	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7427648	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7429990	0.83[AFR][1000 genomes]
rs7430879	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7430913	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618163	0.83[EUR][1000 genomes]
rs7619882	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7620736	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7627645	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7642590	0.93[EUR][1000 genomes]
rs7649981	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7653368	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs777015	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs777017	0.84[EUR][1000 genomes]
rs796566	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs800762	0.82[ASN][1000 genomes]
rs810334	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs936428	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9811277	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812875	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9814961	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9825114	0.84[EUR][1000 genomes]
rs9828959	0.88[EUR][1000 genomes]
rs9842649	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9846062	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9854454	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9860485	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9862913	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	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
9	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4858876	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs4858876	MRPS18AP1	cis	Artery Tibial	GTEx
rs4858876	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs4858876	MRPS18AP1	cis	lung	GTEx
rs4858876	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs4858876	MRPS18AP1	cis	Thyroid	GTEx
rs4858876	ZNF589	cis	Nerve Tibial	GTEx
rs4858876	CDC25A	cis	Muscle Skeletal	GTEx
rs4858876	CDC25A	cis	Thyroid	GTEx
rs4858876	NME6	cis	Esophagus Muscularis	GTEx
rs4858876	ZNF589	cis	Artery Tibial	GTEx
rs4858876	MRPS18AP1	cis	Nerve Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48051200-48128000	Weak transcription	Primary B cells from cord blood	blood
2	chr3:48059600-48128800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:48059800-48090800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:48059800-48093600	Weak transcription	Gastric	stomach
5	chr3:48060800-48088800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:48060800-48089400	Weak transcription	Dnd41	blood
7	chr3:48064400-48128800	Weak transcription	Esophagus	oesophagus
8	chr3:48074800-48105400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:48075800-48102600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:48076200-48094200	Weak transcription	Aorta	Aorta
11	chr3:48076400-48100400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:48077000-48083200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:48078400-48083200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:48079600-48083000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:48080000-48083400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:48080600-48090800	Weak transcription	Lung	lung
17	chr3:48081000-48083000	Weak transcription	Right Atrium	heart
18	chr3:48081000-48083600	Weak transcription	Left Ventricle	heart
19	chr3:48081000-48085000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:48081000-48086000	Weak transcription	Fetal Stomach	stomach
21	chr3:48081000-48089400	Weak transcription	K562	blood
22	chr3:48081000-48090400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:48081000-48090800	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:48081000-48090800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:48081000-48093800	Weak transcription	Pancreas	Pancrea
26	chr3:48081200-48083600	Enhancers	Hela-S3	cervix
27	chr3:48081200-48093600	Weak transcription	Psoas Muscle	Psoas
28	chr3:48081400-48089000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:48081400-48089600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:48081400-48098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:48081400-48110600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:48081400-48128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:48081600-48083000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:48081600-48083000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:48081600-48083000	Weak transcription	GM12878-XiMat	blood
36	chr3:48081600-48083200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:48081600-48083200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:48081600-48083200	Weak transcription	Brain Angular Gyrus	brain
39	chr3:48081600-48083400	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:48081600-48083400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:48081600-48083400	Weak transcription	Brain Substantia Nigra	brain
42	chr3:48081600-48083400	Weak transcription	A549	lung
43	chr3:48081600-48083400	Weak transcription	NH-A	brain
44	chr3:48081600-48083800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:48081600-48089600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:48081600-48090200	Weak transcription	Fetal Lung	lung
47	chr3:48081600-48090400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:48081600-48092000	Weak transcription	Stomach Mucosa	stomach
49	chr3:48081600-48092400	Weak transcription	Brain Germinal Matrix	brain
50	chr3:48081600-48093200	Weak transcription	Colon Smooth Muscle	Colon

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