Variant report

Variant	rs60446735
Chromosome Location	chr3:47971448-47971449
allele	A/G
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	POLR2A	chr3:47971422-47971504	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47970944..47972483-chr3:47977512..47980509,2	K562	blood:

Variant related genes	Relation type
MAP4	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1013431	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1060407	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1061003	0.83[AMR][1000 genomes];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	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1137524	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707679	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11710199	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13074973	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075457	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13075795	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13077230	0.92[ASN][1000 genomes]
rs13081701	0.86[EUR][1000 genomes]
rs13093830	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530646	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1550914	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1665982	0.82[EUR][1000 genomes]
rs1684942	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17290490	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs184388	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053767	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121754	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2166770	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2166772	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631721	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28637561	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2882668	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319680	0.82[EUR][1000 genomes]
rs319681	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319682	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319684	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319685	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319686	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319687	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs319688	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs319689	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319690	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs319691	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs319692	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319693	0.80[ASN][1000 genomes]
rs319694	0.92[ASN][1000 genomes]
rs319695	0.80[ASN][1000 genomes]
rs319696	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34025851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34249203	0.80[ASN][1000 genomes]
rs34750113	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35199727	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35314534	0.89[EUR][1000 genomes]
rs35582375	0.92[ASN][1000 genomes]
rs35689209	0.84[EUR][1000 genomes]
rs35943823	0.82[EUR][1000 genomes]
rs3732529	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];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	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4296617	0.89[EUR][1000 genomes]
rs4392441	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4599334	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858860	0.85[ASN][1000 genomes]
rs4858871	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858876	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858880	0.83[EUR][1000 genomes]
rs4858881	0.82[EUR][1000 genomes]
rs4858887	0.87[EUR][1000 genomes]
rs5012971	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62260764	0.82[EUR][1000 genomes]
rs62263575	0.83[ASN][1000 genomes]
rs6442090	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442091	0.89[EUR][1000 genomes]
rs6442094	0.82[EUR][1000 genomes]
rs6442096	0.83[EUR][1000 genomes]
rs6442101	0.83[EUR][1000 genomes]
rs6770467	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6770477	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772396	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773208	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6783629	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6791834	0.85[EUR][1000 genomes]
rs6803741	0.85[EUR][1000 genomes]
rs6806820	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7374516	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7426976	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7427418	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7429990	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7430879	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7430913	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7619882	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7620736	0.85[EUR][1000 genomes]
rs7627645	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7642590	0.86[EUR][1000 genomes]
rs7649981	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7653368	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs777014	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs777015	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs777017	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs796566	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs800762	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs810334	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811277	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9812875	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814961	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9842649	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846062	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9854454	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860485	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862913	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs60446735	ZNF589	cis	Nerve Tibial	GTEx
rs60446735	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs60446735	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs60446735	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs60446735	MRPS18AP1	cis	Nerve Tibial	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47910200-47978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47952000-47972400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:47952600-47979200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:47953800-47971600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:47957800-47991000	Weak transcription	Fetal Kidney	kidney
6	chr3:47958400-47976800	Weak transcription	Small Intestine	intestine
7	chr3:47958600-47971600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:47958600-47972000	Weak transcription	Brain Substantia Nigra	brain
9	chr3:47958600-47976400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:47958600-47980400	Weak transcription	Pancreas	Pancrea
11	chr3:47958600-47989600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:47958800-47976800	Weak transcription	Fetal Heart	heart
13	chr3:47959000-47981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:47962800-47972400	Weak transcription	Spleen	Spleen
15	chr3:47962800-47988600	Weak transcription	Esophagus	oesophagus
16	chr3:47963000-47991200	Weak transcription	Gastric	stomach
17	chr3:47963400-47971600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:47966200-47991200	Weak transcription	A549	lung
19	chr3:47967000-47974000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:47967000-47981000	Weak transcription	HUVEC	blood vessel
21	chr3:47968400-47976000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:47968400-47981600	Weak transcription	Brain Anterior Caudate	brain
23	chr3:47968600-48012600	Weak transcription	Primary B cells from cord blood	blood
24	chr3:47968800-47980000	Weak transcription	Right Ventricle	heart
25	chr3:47968800-48003000	Weak transcription	Primary T cells from cord blood	blood
26	chr3:47969000-48003000	Weak transcription	Thymus	Thymus
27	chr3:47969200-48002600	Weak transcription	Aorta	Aorta
28	chr3:47969200-48003200	Weak transcription	Lung	lung
29	chr3:47969400-47979800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:47969600-47971600	Weak transcription	Placenta	Placenta
31	chr3:47969600-47972000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:47969600-47980400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:47969600-47982200	Weak transcription	GM12878-XiMat	blood
34	chr3:47969800-47971600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:47969800-47971600	Weak transcription	Dnd41	blood
36	chr3:47969800-47971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:47969800-47971800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:47969800-47972200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:47969800-47973600	Weak transcription	HSMM	muscle
40	chr3:47969800-47974000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:47969800-47974200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:47969800-47974800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:47969800-47977200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:47969800-47977400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr3:47969800-47978600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:47969800-47979800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:47969800-47982000	Weak transcription	Adipose Nuclei	Adipose
48	chr3:47969800-47983400	Weak transcription	Liver	Liver
49	chr3:47969800-47991000	Weak transcription	NHDF-Ad	bronchial
50	chr3:47969800-47991200	Weak transcription	Duodenum Mucosa	Duodenum

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