Variant report

Variant	rs565919
Chromosome Location	chr1:93706713-93706714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1000607	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1057257	0.82[AMR][1000 genomes]
rs1060622	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10782955	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10782957	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10874759	0.81[AMR][1000 genomes]
rs10874762	0.82[AMR][1000 genomes]
rs10874764	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10874772	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10874773	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1088318	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164870	0.82[AMR][1000 genomes]
rs11164871	0.85[AMR][1000 genomes]
rs11164879	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11164881	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11164885	0.81[ASN][1000 genomes]
rs11164902	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164904	0.83[ASN][1000 genomes]
rs11164916	0.82[EUR][1000 genomes]
rs12030549	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12030843	0.81[ASN][1000 genomes]
rs12031765	0.81[ASN][1000 genomes]
rs12038699	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12044557	0.81[ASN][1000 genomes]
rs12118230	0.83[AMR][1000 genomes]
rs12118262	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12124011	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12124771	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12128131	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12133907	0.82[EUR][1000 genomes]
rs12139009	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12139633	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12385720	0.83[AMR][1000 genomes]
rs12752223	0.82[EUR][1000 genomes]
rs1335679	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1474927	0.86[AMR][1000 genomes]
rs1535699	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1535701	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1572343	0.81[AMR][1000 genomes]
rs1856027	0.86[AMR][1000 genomes]
rs1932314	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2031225	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031226	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2114273	0.81[EUR][1000 genomes]
rs2152358	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2208044	0.82[AMR][1000 genomes]
rs2295423	0.88[AMR][1000 genomes]
rs2295424	0.90[AMR][1000 genomes]
rs2296558	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2297707	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2391254	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765545	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35940311	0.82[AMR][1000 genomes]
rs3754184	0.83[AMR][1000 genomes]
rs3754186	0.95[ASN][1000 genomes]
rs3767962	0.84[EUR][1000 genomes]
rs3904665	0.81[ASN][1000 genomes]
rs4000699	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4240966	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4484937	0.81[ASN][1000 genomes]
rs4847398	0.89[AMR][1000 genomes]
rs4847399	0.88[AMR][1000 genomes]
rs4847402	0.81[AMR][1000 genomes]
rs4847406	0.86[ASN][1000 genomes]
rs4847408	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847410	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs531358	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs531514	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs535760	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs547866	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs555161	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs569414	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58354545	0.81[ASN][1000 genomes]
rs602204	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs612037	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61799500	0.81[ASN][1000 genomes]
rs622608	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624131	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs627779	0.81[AMR][1000 genomes]
rs637646	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6541401	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6541404	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs661126	0.80[AFR][1000 genomes]
rs6658257	0.82[EUR][1000 genomes]
rs6680107	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682670	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6688230	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6703310	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs682514	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs687394	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs693737	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72959220	0.81[ASN][1000 genomes]
rs7418101	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7512911	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517363	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7524964	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526112	0.89[ASN][1000 genomes]
rs7537403	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7540025	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7541304	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541687	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7547244	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7551485	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7553465	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7553916	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs797661	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs797666	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs797668	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs797671	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797672	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs797675	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs797676	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs797680	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs797681	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942196	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9432453	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9432459	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9432465	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9432681	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9660390	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs565919	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs565919	RP4-717I23.3	cis	Whole Blood	GTEx
rs565919	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs565919	RP4-717I23.3	cis	Artery Aorta	GTEx
rs565919	RP4-717I23.3	cis	Thyroid	GTEx
rs565919	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs565919	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs565919	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs565919	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs565919	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs565919	RP4-717I23.3	cis	Artery Tibial	GTEx
rs565919	RP4-717I23.3	cis	lung	GTEx
rs565919	DR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:93654200-93708400	Weak transcription	Esophagus	oesophagus
5	chr1:93654600-93708000	Weak transcription	Ovary	ovary
6	chr1:93657600-93708400	Weak transcription	Left Ventricle	heart
7	chr1:93661400-93708200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:93661800-93708200	Weak transcription	Fetal Brain Female	brain
9	chr1:93665400-93708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:93665400-93708400	Weak transcription	Spleen	Spleen
11	chr1:93665600-93707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:93665800-93707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:93668800-93708400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:93672600-93708400	Weak transcription	Placenta	Placenta
16	chr1:93673800-93707400	Weak transcription	A549	lung
17	chr1:93682400-93708800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:93684800-93708400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:93685200-93707400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:93685400-93708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:93685600-93708400	Weak transcription	NH-A	brain
22	chr1:93685600-93709200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:93686600-93708400	Weak transcription	Aorta	Aorta
24	chr1:93686800-93708400	Weak transcription	Fetal Lung	lung
25	chr1:93688200-93714800	Weak transcription	HSMMtube	muscle
26	chr1:93689200-93708400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:93690200-93707400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:93690200-93708600	Weak transcription	NHLF	lung
29	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
31	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:93693400-93709200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:93694200-93707800	Weak transcription	Fetal Stomach	stomach
34	chr1:93700200-93707600	Strong transcription	Primary B cells from cord blood	blood
35	chr1:93702200-93707600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:93702400-93708600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:93703200-93708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:93703400-93706800	Weak transcription	Primary T cells from cord blood	blood
39	chr1:93703400-93707200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:93703400-93708400	Weak transcription	Fetal Intestine Large	intestine
41	chr1:93703600-93709200	Weak transcription	Fetal Heart	heart
42	chr1:93704000-93708400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
44	chr1:93704400-93708400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:93704800-93707200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:93704800-93707800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:93704800-93708400	Weak transcription	HepG2	liver
48	chr1:93704800-93708600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:93704800-93710800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:93705000-93706800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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