Variant report

Variant	rs9660390
Chromosome Location	chr1:93745535-93745536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1000607	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782957	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10874772	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10874773	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1088318	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164902	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164904	0.85[ASN][1000 genomes]
rs12124771	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12139633	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12405487	0.83[ASN][1000 genomes]
rs1535699	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1535701	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031225	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2031226	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296558	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391251	0.83[ASN][1000 genomes]
rs2391254	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3754186	0.84[ASN][1000 genomes]
rs4000699	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240966	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847406	0.88[ASN][1000 genomes]
rs4847408	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847410	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs531514	0.85[ASN][1000 genomes]
rs535760	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs547866	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs565919	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs569414	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs602204	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61799516	0.83[ASN][1000 genomes]
rs622608	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs637646	0.85[ASN][1000 genomes]
rs6541349	0.85[ASN][1000 genomes]
rs6541401	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6541404	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6676902	0.83[ASN][1000 genomes]
rs6680107	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6684908	0.83[ASN][1000 genomes]
rs6703310	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs682514	0.85[ASN][1000 genomes]
rs687394	0.85[ASN][1000 genomes]
rs693737	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7418101	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7512911	0.85[ASN][1000 genomes]
rs7524964	0.86[ASN][1000 genomes]
rs7526112	0.91[ASN][1000 genomes]
rs7537403	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7540025	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541304	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7547244	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7551485	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs797666	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs797668	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs797671	0.83[ASN][1000 genomes]
rs797672	0.85[ASN][1000 genomes]
rs797681	0.85[ASN][1000 genomes]
rs942196	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9432453	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9432459	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9432465	0.86[ASN][1000 genomes]
rs9432681	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[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	nsv946082	chr1:93741885-93761433	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9660390	RP4-717I23.3	cis	Whole Blood	GTEx
rs9660390	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs9660390	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs9660390	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs9660390	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs9660390	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs9660390	RP4-717I23.3	cis	Artery Tibial	GTEx
rs9660390	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs9660390	RP4-717I23.3	cis	lung	GTEx
rs9660390	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs9660390	RP4-717I23.3	cis	Thyroid	GTEx
rs9660390	RP4-717I23.3	cis	Artery Aorta	GTEx
rs9660390	RP4-717I23.3	cis	Nerve Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:93720000-93762000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:93728600-93751400	Weak transcription	Adipose Nuclei	Adipose
6	chr1:93728600-93754800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:93728600-93764400	Weak transcription	Psoas Muscle	Psoas
8	chr1:93728600-93769400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:93728600-93770400	Weak transcription	HSMM	muscle
10	chr1:93728800-93746600	Weak transcription	Aorta	Aorta
11	chr1:93728800-93751600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:93728800-93751800	Weak transcription	Placenta	Placenta
13	chr1:93728800-93752600	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:93728800-93752600	Weak transcription	Fetal Stomach	stomach
15	chr1:93728800-93753800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:93728800-93754800	Weak transcription	Ovary	ovary
17	chr1:93728800-93755000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:93728800-93755000	Weak transcription	Left Ventricle	heart
19	chr1:93728800-93755000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:93728800-93778200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:93729000-93745600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:93729000-93790200	Weak transcription	Osteobl	bone
23	chr1:93729800-93752600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:93729800-93754800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:93729800-93763200	Weak transcription	Pancreas	Pancrea
26	chr1:93730000-93745600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:93730000-93754400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:93730400-93745600	Weak transcription	Fetal Lung	lung
29	chr1:93730400-93745800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:93730400-93748200	Weak transcription	Fetal Thymus	thymus
31	chr1:93730400-93754600	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:93730600-93752600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:93731000-93765400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:93731200-93745600	Weak transcription	Primary B cells from cord blood	blood
35	chr1:93731200-93745600	Weak transcription	GM12878-XiMat	blood
36	chr1:93731200-93787400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:93731600-93745600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:93731600-93747200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:93731800-93752800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:93731800-93754200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:93731800-93754600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:93736400-93771200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:93739200-93755000	Weak transcription	HSMMtube	muscle
44	chr1:93739600-93754200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:93739600-93766600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:93740400-93745800	Weak transcription	Primary T cells from cord blood	blood
47	chr1:93740400-93748600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:93740800-93746800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:93741800-93752600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:93742000-93754400	Weak transcription	Duodenum Mucosa	Duodenum

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