Variant report

Variant	rs34025851
Chromosome Location	chr3:47953733-47953734
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr3:47951498-47953960	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47952765..47954649-chr3:47957193..47959819,2	K562	blood:
2	chr3:47908132..47910392-chr3:47951934..47954399,2	K562	blood:

Variant related genes	Relation type
MAP4	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1013431	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1060407	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1061003	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130150	0.92[ASN][1000 genomes]
rs11130152	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130154	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1137524	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707679	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11710199	0.89[ASN][1000 genomes]
rs13074973	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075457	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13075795	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13077230	0.92[ASN][1000 genomes]
rs13081701	0.86[EUR][1000 genomes]
rs13093830	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530646	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1550914	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1665982	0.82[EUR][1000 genomes]
rs1684942	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17290490	0.92[ASN][1000 genomes]
rs184388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053767	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121754	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2166770	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2166772	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631721	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28637561	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2882668	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319680	0.82[EUR][1000 genomes]
rs319681	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319682	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319684	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319685	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319686	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319687	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs319688	0.94[EUR][1000 genomes]
rs319689	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319690	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs319691	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs319692	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319693	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs319694	0.92[ASN][1000 genomes]
rs319695	0.80[ASN][1000 genomes]
rs319696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34249203	0.80[ASN][1000 genomes]
rs34750113	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35199727	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35314534	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35582375	0.92[ASN][1000 genomes]
rs35689209	0.84[EUR][1000 genomes]
rs35943823	0.82[EUR][1000 genomes]
rs3732529	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772399	0.85[ASN][1000 genomes]
rs3888	0.85[ASN][1000 genomes]
rs3915654	0.85[ASN][1000 genomes]
rs4293721	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4296617	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4392441	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4599334	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858860	0.85[ASN][1000 genomes]
rs4858871	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858876	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858880	0.83[EUR][1000 genomes]
rs4858881	0.82[EUR][1000 genomes]
rs4858887	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5012971	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60446735	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260764	0.82[EUR][1000 genomes]
rs62263575	0.83[ASN][1000 genomes]
rs6442090	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442091	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6442094	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6442096	0.83[EUR][1000 genomes]
rs6442101	0.83[EUR][1000 genomes]
rs6770467	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6770477	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772396	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773208	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6783629	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6791834	0.85[EUR][1000 genomes]
rs6803741	0.85[EUR][1000 genomes]
rs6806820	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7374516	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7426976	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7427418	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7429990	0.82[EUR][1000 genomes]
rs7430879	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7430913	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7619882	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7620736	0.85[EUR][1000 genomes]
rs7627645	0.87[EUR][1000 genomes]
rs7642590	0.86[EUR][1000 genomes]
rs7649981	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7653368	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs777014	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs777015	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs777017	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs796566	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs800762	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs810334	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811277	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9812875	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814961	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9842649	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846062	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9854454	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860485	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862913	0.89[EUR][1000 genomes];0.91[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	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
2	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
3	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
4	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
5	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
6	esv1796001	chr3:47912703-48012797	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1826403	chr3:47912703-48012797	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv1000817	chr3:47927730-48032401	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	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
12	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs34025851	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs34025851	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs34025851	MRPS18AP1	cis	lung	GTEx
rs34025851	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs34025851	MRPS18AP1	cis	Nerve Tibial	GTEx
rs34025851	ZNF589	cis	Nerve Tibial	GTEx
rs34025851	NME6	cis	Esophagus Muscularis	GTEx
rs34025851	MRPS18AP1	cis	Thyroid	GTEx
rs34025851	ZNF589	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47910200-47957000	Weak transcription	Small Intestine	intestine
2	chr3:47910200-47978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:47917600-47957400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:47926800-47957400	Weak transcription	Colonic Mucosa	Colon
5	chr3:47932000-47969200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:47934200-47957200	Weak transcription	Gastric	stomach
7	chr3:47934800-47956800	Weak transcription	Fetal Brain Female	brain
8	chr3:47935200-47957200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:47935800-47956200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:47935800-47956800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:47941400-47954600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:47941400-47954800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:47941400-47968000	Weak transcription	Stomach Mucosa	stomach
14	chr3:47942600-47963600	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:47943000-47957200	Weak transcription	Fetal Heart	heart
16	chr3:47943200-47957200	Weak transcription	Aorta	Aorta
17	chr3:47943400-47957000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:47945800-47957400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:47946600-47956200	Weak transcription	Pancreas	Pancrea
20	chr3:47947600-47959600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:47947800-47953800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:47948200-47956200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:47948400-47959400	Strong transcription	Fetal Intestine Large	intestine
24	chr3:47948600-47970800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:47948800-47959400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:47949000-47954000	Strong transcription	Primary T cells from cord blood	blood
27	chr3:47949000-47958800	Strong transcription	Primary B cells from cord blood	blood
28	chr3:47949000-47959600	Strong transcription	Adipose Nuclei	Adipose
29	chr3:47949000-47960800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:47949200-47953800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr3:47949200-47955200	Strong transcription	HepG2	liver
32	chr3:47949600-47957400	Weak transcription	Brain Angular Gyrus	brain
33	chr3:47949600-47963200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:47949600-47970000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:47949800-47957200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:47949800-47958800	Strong transcription	GM12878-XiMat	blood
37	chr3:47950200-47954000	Strong transcription	Lung	lung
38	chr3:47950400-47955800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:47950400-47959200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:47950400-47959600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:47950400-47963800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:47950600-47954200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:47950600-47957200	Weak transcription	Right Atrium	heart
44	chr3:47950600-47963400	Strong transcription	Fetal Thymus	thymus
45	chr3:47951000-47954000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:47951000-47954200	Genic enhancers	NH-A	brain
47	chr3:47951000-47957800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:47951000-47959400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:47951200-47953800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:47951200-47954000	Strong transcription	Fetal Stomach	stomach

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