Variant report

Variant	rs520600
Chromosome Location	chr3:191104100-191104101
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1066857	0.94[ASN][1000 genomes]
rs13061649	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs150505	0.93[ASN][1000 genomes]
rs1656143	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662184	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs167148	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1715641	0.98[ASN][1000 genomes]
rs176821	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176822	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184140	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1850961	0.87[ASN][1000 genomes]
rs186064	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs186065	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs186068	0.92[ASN][1000 genomes]
rs211043	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572064	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293800	0.87[AFR][1000 genomes]
rs293805	0.87[AFR][1000 genomes]
rs293806	0.87[AFR][1000 genomes]
rs293807	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293808	0.87[AFR][1000 genomes]
rs293809	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293810	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293811	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293812	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293813	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293814	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293816	0.88[ASN][1000 genomes]
rs293817	0.88[ASN][1000 genomes]
rs293837	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293839	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293840	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293841	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293852	0.95[ASN][1000 genomes]
rs293854	0.95[ASN][1000 genomes]
rs293856	0.95[ASN][1000 genomes]
rs293857	0.95[ASN][1000 genomes]
rs293858	0.95[ASN][1000 genomes]
rs293859	0.93[ASN][1000 genomes]
rs293861	0.93[ASN][1000 genomes]
rs364519	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs367747	0.87[AFR][1000 genomes]
rs369174	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs381090	0.80[EUR][1000 genomes]
rs383075	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs383529	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs386241	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs389765	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs390744	0.87[AFR][1000 genomes]
rs392311	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs399575	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs403078	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs407226	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs415149	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs420266	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs423989	0.93[ASN][1000 genomes]
rs429374	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429521	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434556	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs436393	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs436428	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438589	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs440266	0.93[ASN][1000 genomes]
rs441509	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445914	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs447931	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs449398	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491252	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497918	0.90[ASN][1000 genomes]
rs513632	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs520494	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529523	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs566548	0.93[AFR][1000 genomes]
rs568702	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs578401	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6953	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs695910	0.87[ASN][1000 genomes]
rs696347	0.93[ASN][1000 genomes]
rs696348	0.92[ASN][1000 genomes]
rs696349	0.93[ASN][1000 genomes]
rs697905	0.87[AFR][1000 genomes]
rs697913	0.91[ASN][1000 genomes]
rs709142	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs520600	CCDC50	cis	Artery Aorta	GTEx
rs520600	CCDC50	cis	Artery Tibial	GTEx
rs520600	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
2	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:191079600-191121200	Weak transcription	Gastric	stomach
5	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
7	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:191087800-191109200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:191088000-191109800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
14	chr3:191094800-191114800	Weak transcription	A549	lung
15	chr3:191095000-191107600	Weak transcription	Fetal Intestine Small	intestine
16	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:191096400-191109600	Weak transcription	Brain Angular Gyrus	brain
18	chr3:191096600-191105800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:191096600-191114800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:191097200-191109200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:191098000-191111400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:191099400-191107000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
24	chr3:191099600-191113800	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:191099600-191114000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:191099600-191114600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:191099800-191104200	Weak transcription	HepG2	liver
29	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:191100200-191106000	Weak transcription	Left Ventricle	heart
31	chr3:191100200-191106800	Weak transcription	Brain Germinal Matrix	brain
32	chr3:191100200-191107200	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:191100200-191108200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:191100200-191108400	Weak transcription	Ovary	ovary
35	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
36	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
37	chr3:191100200-191119600	Weak transcription	K562	blood
38	chr3:191100400-191107200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:191100400-191108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:191100400-191114000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
42	chr3:191100400-191117400	Weak transcription	Lung	lung
43	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
44	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
45	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
46	chr3:191100600-191107200	Weak transcription	Aorta	Aorta
47	chr3:191100600-191107400	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:191100600-191109400	Weak transcription	Primary T cells from cord blood	blood
49	chr3:191100800-191115400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:191101000-191107400	Weak transcription	Placenta	Placenta

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