Variant report

Variant	rs785513
Chromosome Location	chr1:46538320-46538321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46528747..46531379-chr1:46537742..46540371,2	K562	blood:
2	chr1:46536821..46539157-chr1:46549967..46552900,2	K562	blood:
3	chr1:46532903..46538508-chr1:46540157..46543502,7	K562	blood:

Extended variants
information (count: 157 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1085240	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1085242	0.91[ASN][1000 genomes]
rs1085244	0.90[ASN][1000 genomes]
rs10890380	0.82[EUR][1000 genomes]
rs10890381	0.82[EUR][1000 genomes]
rs10890382	0.85[EUR][1000 genomes]
rs11211235	0.81[EUR][1000 genomes]
rs11211236	0.81[EUR][1000 genomes]
rs11211237	0.82[EUR][1000 genomes]
rs11211238	0.82[EUR][1000 genomes]
rs11211239	0.84[EUR][1000 genomes]
rs11211244	0.84[EUR][1000 genomes]
rs11211248	0.85[EUR][1000 genomes]
rs11211251	0.94[ASN][1000 genomes]
rs11211252	0.94[ASN][1000 genomes]
rs12067716	0.81[EUR][1000 genomes]
rs12077546	0.81[EUR][1000 genomes]
rs12097799	0.82[EUR][1000 genomes]
rs12124291	0.81[EUR][1000 genomes]
rs12403666	0.81[EUR][1000 genomes]
rs1355642	0.82[ASN][1000 genomes]
rs1588663	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1612419	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1613296	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1622208	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1707303	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1707304	0.83[ASN][1000 genomes]
rs1707317	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1707321	0.94[ASN][1000 genomes]
rs1707322	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1707333	0.94[ASN][1000 genomes]
rs1707335	0.88[ASN][1000 genomes]
rs1707337	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1707338	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1707339	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1707340	0.94[ASN][1000 genomes]
rs1768800	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1768801	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1768802	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1768803	0.96[ASN][1000 genomes]
rs1768807	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1768815	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1768816	0.95[ASN][1000 genomes]
rs1768817	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1768818	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2297883	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2458400	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2486447	0.94[ASN][1000 genomes]
rs2669156	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3922886	0.85[EUR][1000 genomes]
rs3922887	0.85[EUR][1000 genomes]
rs4073847	0.85[EUR][1000 genomes]
rs4459051	0.82[EUR][1000 genomes]
rs4460583	0.82[EUR][1000 genomes]
rs4489497	0.81[EUR][1000 genomes]
rs4660328	0.81[EUR][1000 genomes]
rs4660331	0.84[EUR][1000 genomes]
rs4660332	0.84[EUR][1000 genomes]
rs4660334	0.84[EUR][1000 genomes]
rs4660335	0.85[EUR][1000 genomes]
rs4660336	0.88[EUR][1000 genomes]
rs4660903	0.84[EUR][1000 genomes]
rs4660904	0.84[EUR][1000 genomes]
rs4660905	0.84[EUR][1000 genomes]
rs4660906	0.85[EUR][1000 genomes]
rs4660910	0.94[ASN][1000 genomes]
rs4660911	0.90[ASN][1000 genomes]
rs61785613	0.81[EUR][1000 genomes]
rs61785614	0.82[EUR][1000 genomes]
rs6429588	0.84[EUR][1000 genomes]
rs6661500	0.85[EUR][1000 genomes]
rs6662641	0.88[ASN][1000 genomes]
rs6671754	0.80[EUR][1000 genomes]
rs6675259	0.93[EUR][1000 genomes]
rs6675726	0.91[ASN][1000 genomes]
rs6677777	0.85[EUR][1000 genomes]
rs7532204	0.88[EUR][1000 genomes]
rs7534331	0.81[EUR][1000 genomes]
rs7538978	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs785462	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs785463	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785464	0.96[ASN][1000 genomes]
rs785465	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785466	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785467	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785468	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785469	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785470	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785471	0.94[ASN][1000 genomes]
rs785472	0.94[ASN][1000 genomes]
rs785473	0.94[ASN][1000 genomes]
rs785477	0.84[EUR][1000 genomes]
rs785478	0.88[EUR][1000 genomes]
rs785480	0.88[EUR][1000 genomes]
rs785481	0.93[ASN][1000 genomes]
rs785482	0.91[ASN][1000 genomes]
rs785483	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs785484	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs785485	0.88[ASN][1000 genomes]
rs785486	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs785488	0.88[ASN][1000 genomes]
rs785489	0.88[ASN][1000 genomes]
rs785490	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs785491	0.88[ASN][1000 genomes]
rs785492	0.88[ASN][1000 genomes]
rs785493	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs785494	0.88[ASN][1000 genomes]
rs785495	0.88[ASN][1000 genomes]
rs785496	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs785497	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs785498	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs785499	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs785500	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs785501	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs785502	0.87[ASN][1000 genomes]
rs785503	0.87[ASN][1000 genomes]
rs785504	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs785506	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs785507	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs785508	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs785509	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs785510	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785511	0.96[ASN][1000 genomes]
rs785512	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs785516	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs785517	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs785518	0.84[AMR][1000 genomes]
rs785519	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs785520	0.88[ASN][1000 genomes]
rs796773	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs809774	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs809775	0.97[ASN][1000 genomes]
rs814168	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs925524	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9429088	0.83[ASN][1000 genomes]
rs9429094	0.83[ASN][1000 genomes]
rs9429183	0.94[ASN][1000 genomes]
rs9429186	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9429189	0.86[ASN][1000 genomes]
rs946524	0.88[EUR][1000 genomes]
rs946525	0.88[EUR][1000 genomes]
rs946527	0.86[EUR][1000 genomes]
rs946528	0.83[EUR][1000 genomes]
rs9793167	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1009474	chr1:46320433-46557734	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1007750	chr1:46471293-46552564	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs785513	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs785513	NSUN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46501400-46548200	Weak transcription	Aorta	Aorta
2	chr1:46506000-46549400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:46508400-46546600	Weak transcription	HSMMtube	muscle
4	chr1:46509600-46540200	Weak transcription	Spleen	Spleen
5	chr1:46510400-46548400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:46518200-46551600	Weak transcription	Psoas Muscle	Psoas
7	chr1:46524800-46547000	Weak transcription	Lung	lung
8	chr1:46525200-46543000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:46525400-46548800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:46525600-46552600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:46527600-46542400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:46527600-46543400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:46527800-46543000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:46527800-46546400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:46527800-46550400	Weak transcription	Fetal Heart	heart
16	chr1:46528600-46540200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:46528600-46552200	Weak transcription	Thymus	Thymus
18	chr1:46528800-46550400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:46529000-46543200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:46529000-46549800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:46529400-46545200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:46529400-46545400	Weak transcription	Small Intestine	intestine
23	chr1:46531200-46543800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:46531400-46543600	Weak transcription	Fetal Brain Male	brain
25	chr1:46531400-46543600	Weak transcription	HSMM	muscle
26	chr1:46531400-46543800	Weak transcription	Primary T cells from cord blood	blood
27	chr1:46531400-46546600	Weak transcription	HUVEC	blood vessel
28	chr1:46531600-46541000	Weak transcription	Fetal Intestine Small	intestine
29	chr1:46531600-46543000	Weak transcription	Fetal Intestine Large	intestine
30	chr1:46531800-46547200	Weak transcription	Adipose Nuclei	Adipose
31	chr1:46532400-46575200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:46532600-46540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:46532600-46543800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:46532800-46543200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:46532800-46547200	Weak transcription	Right Ventricle	heart
36	chr1:46533400-46550200	Weak transcription	NH-A	brain
37	chr1:46533800-46542000	Weak transcription	Fetal Kidney	kidney
38	chr1:46534400-46543600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:46535000-46542200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:46535200-46547000	Weak transcription	Placenta	Placenta
41	chr1:46535200-46547000	Weak transcription	Fetal Stomach	stomach
42	chr1:46536200-46539000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:46536200-46540000	Weak transcription	Fetal Brain Female	brain
44	chr1:46536400-46538800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:46536400-46538800	Weak transcription	Dnd41	blood
46	chr1:46536400-46540000	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:46536400-46540800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:46536400-46547400	Weak transcription	Fetal Lung	lung
49	chr1:46536600-46540200	Weak transcription	GM12878-XiMat	blood
50	chr1:46536600-46543000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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