Variant report

Variant	rs4858879
Chromosome Location	chr3:48064367-48064368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48063591..48066212-chr3:48130578..48132511,2	K562	blood:
2	chr3:48058679..48060813-chr3:48062111..48064582,2	K562	blood:
3	chr3:48058931..48061886-chr3:48063600..48066605,3	MCF-7	breast:
4	chr3:48063591..48066767-chr3:48129911..48132511,3	K562	blood:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11720973	0.81[AMR][1000 genomes]
rs35979968	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62260764	0.94[ASN][1000 genomes]
rs7651237	0.91[AMR][1000 genomes];0.90[EUR][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4858879	CDC25A	cis	Thyroid	GTEx
rs4858879	ZNF589	cis	Artery Tibial	GTEx
rs4858879	ZNF589	cis	Thyroid	GTEx
rs4858879	ZNF589	cis	Nerve Tibial	GTEx
rs4858879	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs4858879	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs4858879	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs4858879	ZNF589	cis	Esophagus Mucosa	GTEx
rs4858879	MRPS18AP1	cis	Artery Tibial	GTEx
rs4858879	CDC25A	cis	Artery Tibial	GTEx
rs4858879	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs4858879	MRPS18AP1	cis	Nerve Tibial	GTEx
rs4858879	MRPS18AP1	cis	Thyroid	GTEx
rs4858879	NME6	cis	Esophagus Muscularis	GTEx
rs4858879	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:94 , 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	chr3:48051600-48065000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:48053600-48075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:48055600-48075200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:48056200-48076000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:48057800-48065000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:48058000-48064800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:48058000-48065000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:48058200-48064600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:48058400-48064600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:48058400-48067600	Weak transcription	Fetal Lung	lung
14	chr3:48058400-48082400	Weak transcription	Spleen	Spleen
15	chr3:48058600-48064400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:48058600-48064400	Weak transcription	Brain Angular Gyrus	brain
17	chr3:48058800-48068400	Weak transcription	Small Intestine	intestine
18	chr3:48058800-48075600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:48058800-48080600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:48059000-48064400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:48059200-48064600	Weak transcription	Fetal Kidney	kidney
22	chr3:48059200-48065000	Weak transcription	Aorta	Aorta
23	chr3:48059200-48080600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:48059400-48064400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:48059400-48075200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:48059600-48128800	Weak transcription	Primary T cells from cord blood	blood
27	chr3:48059800-48064600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:48059800-48066800	Weak transcription	Lung	lung
29	chr3:48059800-48068400	Weak transcription	Right Ventricle	heart
30	chr3:48059800-48068800	Weak transcription	Right Atrium	heart
31	chr3:48059800-48090800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:48059800-48093600	Weak transcription	Gastric	stomach
33	chr3:48060000-48068400	Weak transcription	Liver	Liver
34	chr3:48060000-48075400	Weak transcription	Hela-S3	cervix
35	chr3:48060200-48064600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:48060600-48064600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:48060600-48064800	Weak transcription	Stomach Mucosa	stomach
38	chr3:48060600-48065000	Weak transcription	NH-A	brain
39	chr3:48060800-48064400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:48060800-48064400	Weak transcription	NHLF	lung
41	chr3:48060800-48064600	Weak transcription	A549	lung
42	chr3:48060800-48088800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:48060800-48089400	Weak transcription	Dnd41	blood
44	chr3:48061200-48064400	Weak transcription	Fetal Intestine Small	intestine
45	chr3:48061200-48064800	Weak transcription	Osteobl	bone
46	chr3:48061200-48068400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:48061400-48064400	Weak transcription	HepG2	liver
48	chr3:48061400-48064600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:48061400-48064800	Weak transcription	HSMMtube	muscle
50	chr3:48061400-48064800	Weak transcription	NHDF-Ad	bronchial

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