Variant report

Variant	rs34507589
Chromosome Location	chr3:47874042-47874043
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47873536..47875559-chr3:48191736..48194650,2	MCF-7	breast:
2	chr3:47871108..47875546-chr3:47876904..47881221,5	K562	blood:
3	chr3:47872432..47874998-chr3:47877284..47880049,4	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11709289	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13072132	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1665982	0.82[EUR][1000 genomes]
rs319680	0.82[EUR][1000 genomes]
rs34448818	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35943823	0.82[EUR][1000 genomes]
rs5016900	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62260764	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7429990	0.82[EUR][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	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
2	nsv1006560	chr3:47867461-48037031	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs34507589	MRPS18AP1	cis	Thyroid	GTEx
rs34507589	MRPS18AP1	cis	Nerve Tibial	GTEx
rs34507589	NME6	cis	Esophagus Muscularis	GTEx
rs34507589	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs34507589	ZNF589	cis	Nerve Tibial	GTEx
rs34507589	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs34507589	MRPS18AP1	cis	Artery Tibial	GTEx
rs34507589	ZNF589	cis	Esophagus Muscularis	GTEx
rs34507589	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs34507589	ZNF589	cis	Artery Tibial	GTEx
rs34507589	CDC25A	cis	Muscle Skeletal	GTEx
rs34507589	MAP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47867800-47882000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:47867800-47882000	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:47867800-47882400	Weak transcription	Small Intestine	intestine
4	chr3:47867800-47882400	Weak transcription	Stomach Mucosa	stomach
5	chr3:47867800-47882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:47867800-47899200	Strong transcription	Fetal Brain Female	brain
7	chr3:47867800-47918800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:47868000-47882200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:47868000-47882800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:47868000-47903000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:47868000-47915200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:47868200-47878600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:47868200-47879400	Weak transcription	Right Atrium	heart
14	chr3:47868200-47882000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:47868200-47882800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:47868200-47892200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:47868200-47902400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:47868400-47874200	Strong transcription	Brain Angular Gyrus	brain
19	chr3:47868400-47876400	Strong transcription	Brain Substantia Nigra	brain
20	chr3:47868400-47881800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:47868400-47882000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr3:47868400-47882000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:47868400-47884400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:47868400-47891000	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:47868400-47891200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr3:47868400-47891400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:47868400-47899200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr3:47868400-47901200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:47868400-47902400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:47868400-47903000	Strong transcription	Placenta	Placenta
31	chr3:47868400-47903400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:47868400-47903400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:47868400-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:47868400-47919000	Strong transcription	Fetal Stomach	stomach
35	chr3:47868600-47874400	Strong transcription	Ovary	ovary
36	chr3:47868600-47876200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:47868600-47879400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:47868600-47880800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:47868600-47882400	Weak transcription	Fetal Heart	heart
40	chr3:47868600-47893600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:47868600-47899000	Strong transcription	Thymus	Thymus
42	chr3:47868600-47899200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:47868600-47899200	Strong transcription	Primary T cells from cord blood	blood
44	chr3:47868600-47899400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:47868600-47901800	Strong transcription	Fetal Intestine Large	intestine
46	chr3:47868600-47902200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:47868600-47902600	Strong transcription	Liver	Liver
48	chr3:47868600-47902800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:47868600-47912200	Strong transcription	Fetal Intestine Small	intestine
50	chr3:47868800-47874200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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