Variant report

Variant	rs7429990
Chromosome Location	chr3:47901803-47901804
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47895316..47897321-chr3:47900052..47901819,3	K562	blood:
2	chr3:47893361..47897321-chr3:47899658..47903190,4	K562	blood:
3	chr3:47899451..47902057-chr3:48195294..48197379,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1013431	0.81[AFR][1000 genomes]
rs1060407	0.82[EUR][1000 genomes]
rs1061003	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1137524	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11707679	0.82[EUR][1000 genomes]
rs13093830	0.82[EUR][1000 genomes]
rs1530646	0.84[AFR][1000 genomes]
rs1550914	0.92[AFR][1000 genomes]
rs1665982	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1684942	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17290490	0.80[AFR][1000 genomes]
rs184388	0.82[EUR][1000 genomes]
rs2166770	0.84[AFR][1000 genomes]
rs2166772	0.84[AFR][1000 genomes]
rs2631721	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs319680	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs319681	0.84[EUR][1000 genomes]
rs319682	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs319684	0.82[EUR][1000 genomes]
rs319685	0.82[EUR][1000 genomes]
rs319686	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs319687	0.81[AFR][1000 genomes]
rs319689	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs319690	0.83[EUR][1000 genomes]
rs319692	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs319694	0.80[AFR][1000 genomes]
rs319696	0.82[EUR][1000 genomes]
rs34025851	0.82[EUR][1000 genomes]
rs34507589	0.82[EUR][1000 genomes]
rs34750113	0.81[EUR][1000 genomes]
rs35199727	0.82[EUR][1000 genomes]
rs35943823	0.99[EUR][1000 genomes]
rs3732529	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4858871	0.82[EUR][1000 genomes]
rs4858876	0.83[AFR][1000 genomes]
rs60446735	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62260764	0.85[EUR][1000 genomes]
rs6772396	0.82[EUR][1000 genomes]
rs7374516	0.90[AFR][1000 genomes]
rs7426976	0.82[AFR][1000 genomes]
rs7619882	0.81[EUR][1000 genomes]
rs777014	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs777015	0.82[EUR][1000 genomes]
rs777017	0.82[EUR][1000 genomes]
rs796566	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs800762	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs810334	0.82[EUR][1000 genomes]
rs9812875	0.81[EUR][1000 genomes]
rs9846062	0.86[AFR][1000 genomes]
rs9854454	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1011662	chr3:47891634-48019462	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv536561	chr3:47891634-48019462	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7429990	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs7429990	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs7429990	ZNF589	cis	Nerve Tibial	GTEx
rs7429990	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs7429990	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs7429990	CDC25A	cis	Muscle Skeletal	GTEx
rs7429990	MRPS18AP1	cis	Nerve Tibial	GTEx
rs7429990	ZNF589	cis	Artery Tibial	GTEx
rs7429990	ZNF589	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47867800-47918800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:47868000-47903000	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:47868000-47915200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47868200-47902400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:47868400-47902400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:47868400-47903000	Strong transcription	Placenta	Placenta
7	chr3:47868400-47903400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:47868400-47903400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:47868400-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:47868400-47919000	Strong transcription	Fetal Stomach	stomach
11	chr3:47868600-47902200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:47868600-47902600	Strong transcription	Liver	Liver
13	chr3:47868600-47902800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:47868600-47912200	Strong transcription	Fetal Intestine Small	intestine
15	chr3:47868800-47902000	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:47868800-47902200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:47868800-47902400	Strong transcription	Osteobl	bone
18	chr3:47869000-47902400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:47869000-47918600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:47869200-47902200	Strong transcription	Dnd41	blood
21	chr3:47870800-47931800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:47877200-47903400	Strong transcription	Lung	lung
23	chr3:47877400-47902600	Strong transcription	Spleen	Spleen
24	chr3:47878800-47908400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:47879800-47902400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:47881200-47902200	Strong transcription	Colon Smooth Muscle	Colon
27	chr3:47881600-47902200	Strong transcription	Esophagus	oesophagus
28	chr3:47881600-47902200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:47881600-47903400	Strong transcription	NHEK	skin
30	chr3:47881800-47902200	Strong transcription	Right Ventricle	heart
31	chr3:47882000-47902200	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr3:47882000-47902200	Strong transcription	NHLF	lung
33	chr3:47882200-47903000	Strong transcription	Ovary	ovary
34	chr3:47882200-47903600	Strong transcription	Left Ventricle	heart
35	chr3:47884600-47918400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:47885000-47902200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:47885000-47914800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:47889800-47910000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:47889800-47912600	Weak transcription	Fetal Heart	heart
40	chr3:47891000-47908400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:47891200-47903200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:47891200-47908600	Weak transcription	Fetal Kidney	kidney
43	chr3:47891400-47909600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:47891400-47912000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:47891600-47903600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:47892000-47902600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr3:47892200-47906800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:47893200-47902200	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:47893600-47906600	Weak transcription	Small Intestine	intestine
50	chr3:47894200-47912200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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