Variant report

Variant	rs1530646
Chromosome Location	chr3:48069648-48069649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48068743..48070956-chr3:48072817..48074815,2	K562	blood:
2	chr3:48067946..48070956-chr3:48070996..48074815,4	K562	blood:

Extended variants
information (count: 130 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1013431	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10446426	0.84[ASN][1000 genomes]
rs1060407	0.89[EUR][1000 genomes]
rs1061003	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130152	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130154	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130155	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1137524	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11707679	0.89[EUR][1000 genomes]
rs11710866	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11711129	0.85[EUR][1000 genomes]
rs11714518	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11720151	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11924107	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12486714	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12493348	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13074973	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13075457	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13075795	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13080997	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13081463	0.85[EUR][1000 genomes]
rs13081701	0.80[EUR][1000 genomes]
rs13093830	0.89[EUR][1000 genomes]
rs1550914	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1684942	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs184388	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2053767	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2121754	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2166770	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2166772	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2361683	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2361684	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2631721	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28637561	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2882668	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs319681	0.84[EUR][1000 genomes]
rs319682	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319684	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319685	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319686	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319687	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319688	0.84[EUR][1000 genomes]
rs319689	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319690	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs319691	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319692	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319696	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34025851	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34597784	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34750113	0.88[EUR][1000 genomes]
rs35199727	0.89[EUR][1000 genomes]
rs35314534	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35689209	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3732529	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4293721	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4296617	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4392441	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4599334	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858871	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858876	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858880	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4858881	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4858882	0.86[EUR][1000 genomes]
rs4858887	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5012971	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56067795	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60446735	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62260830	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6442090	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442091	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6442094	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442096	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442101	0.93[EUR][1000 genomes]
rs6442102	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6766641	0.85[EUR][1000 genomes]
rs6768318	0.86[EUR][1000 genomes]
rs6770467	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770477	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772396	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6773208	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6777081	0.82[EUR][1000 genomes]
rs6783629	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6791834	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6803741	0.95[EUR][1000 genomes]
rs6806820	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7374482	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7374516	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7426976	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7427418	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7427648	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7429990	0.84[AFR][1000 genomes]
rs7430879	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7430913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618163	0.82[EUR][1000 genomes]
rs7619882	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7620736	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7627645	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7642590	0.96[EUR][1000 genomes]
rs7649981	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7651237	0.80[EUR][1000 genomes]
rs7653368	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs777014	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs777015	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs777017	0.89[EUR][1000 genomes]
rs796566	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs800762	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs810334	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs936428	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9811277	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9812875	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9814961	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9825114	0.86[EUR][1000 genomes]
rs9828959	0.89[EUR][1000 genomes]
rs9842649	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9846062	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854454	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9860485	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9862913	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv3335628	chr3:48010796-48074001	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
rs1530646	CDC25A	cis	Thyroid	GTEx
rs1530646	ZNF589	cis	Artery Tibial	GTEx
rs1530646	MRPS18AP1	cis	Nerve Tibial	GTEx
rs1530646	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs1530646	MRPS18AP1	cis	Thyroid	GTEx
rs1530646	ZNF589	cis	Nerve Tibial	GTEx
rs1530646	CDC25A	cis	Muscle Skeletal	GTEx
rs1530646	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs1530646	NME6	cis	Esophagus Muscularis	GTEx
rs1530646	MRPS18AP1	cis	Artery Tibial	GTEx
rs1530646	MRPS18AP1	cis	lung	GTEx
rs1530646	DHX30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48043800-48075200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:48043800-48075200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:48051200-48128000	Weak transcription	Primary B cells from cord blood	blood
4	chr3:48053600-48075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:48055600-48075200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:48056200-48076000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:48058400-48082400	Weak transcription	Spleen	Spleen
8	chr3:48058800-48075600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:48058800-48080600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:48059200-48080600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:48059400-48075200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:48059600-48128800	Weak transcription	Primary T cells from cord blood	blood
13	chr3:48059800-48090800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:48059800-48093600	Weak transcription	Gastric	stomach
15	chr3:48060000-48075400	Weak transcription	Hela-S3	cervix
16	chr3:48060800-48088800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:48060800-48089400	Weak transcription	Dnd41	blood
18	chr3:48062000-48073200	Weak transcription	K562	blood
19	chr3:48062400-48074800	Weak transcription	HSMM	muscle
20	chr3:48063800-48073200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:48064400-48071800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:48064400-48128800	Weak transcription	Esophagus	oesophagus
23	chr3:48064600-48074800	Weak transcription	GM12878-XiMat	blood
24	chr3:48065000-48074600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:48065200-48074600	Weak transcription	Adipose Nuclei	Adipose
26	chr3:48065200-48075200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:48065200-48080600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:48065400-48074600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:48065400-48075200	Weak transcription	HSMMtube	muscle
30	chr3:48065600-48070400	Weak transcription	Fetal Intestine Large	intestine
31	chr3:48066600-48071800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:48066600-48074200	Weak transcription	NHDF-Ad	bronchial
33	chr3:48067200-48075200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:48067600-48069800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:48068000-48077600	Weak transcription	Fetal Lung	lung
36	chr3:48068200-48069800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:48068200-48069800	Enhancers	Fetal Heart	heart
38	chr3:48068400-48069800	Enhancers	Fetal Muscle Leg	muscle
39	chr3:48068800-48069800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:48068800-48074800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:48069000-48069800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:48069000-48069800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:48069000-48072600	Weak transcription	Stomach Mucosa	stomach
44	chr3:48069000-48073200	Weak transcription	Brain Angular Gyrus	brain
45	chr3:48069000-48073200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:48069000-48073200	Weak transcription	Brain Substantia Nigra	brain
47	chr3:48069000-48074200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:48069000-48074600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:48069000-48074600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:48069000-48075000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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