Variant report

Variant	rs682514
Chromosome Location	chr1:93719430-93719431
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93717824..93719584-chr1:93817437..93819207,2	K562	blood:

Extended variants
information (count: 130 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1000607	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1057257	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10782955	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10782957	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10874759	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10874762	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10874764	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10874772	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10874773	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10874777	0.86[EUR][1000 genomes]
rs1088318	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164876	0.84[EUR][1000 genomes]
rs11164879	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164880	0.87[EUR][1000 genomes]
rs11164881	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164885	0.83[ASN][1000 genomes]
rs11164902	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164904	0.88[ASN][1000 genomes]
rs11576494	0.84[EUR][1000 genomes]
rs12030549	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12030843	0.83[ASN][1000 genomes]
rs12031765	0.83[ASN][1000 genomes]
rs12044557	0.83[ASN][1000 genomes]
rs12044657	0.87[EUR][1000 genomes]
rs12044883	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12048219	0.82[ASN][1000 genomes]
rs12118230	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12118262	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12124011	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12124771	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12130734	0.84[EUR][1000 genomes]
rs12133576	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12139633	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12406245	0.86[EUR][1000 genomes]
rs12752223	0.81[ASN][1000 genomes]
rs1335679	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1426318	0.86[EUR][1000 genomes]
rs1535699	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1535701	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1559828	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1572343	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1593512	0.86[EUR][1000 genomes]
rs1932314	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2031225	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2031226	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2152358	0.82[AMR][1000 genomes]
rs2296558	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297707	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2391254	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2765545	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35940311	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3754186	0.97[ASN][1000 genomes]
rs3767962	0.82[ASN][1000 genomes]
rs3767964	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3904665	0.83[ASN][1000 genomes]
rs4000699	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240966	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4484937	0.83[ASN][1000 genomes]
rs4847235	0.84[EUR][1000 genomes]
rs4847240	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847402	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4847406	0.91[ASN][1000 genomes]
rs4847408	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847410	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847412	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847419	0.86[EUR][1000 genomes]
rs4847420	0.86[EUR][1000 genomes]
rs531358	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs531514	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs535760	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs547866	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs555161	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs565919	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs569414	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58354545	0.83[ASN][1000 genomes]
rs59417472	0.86[EUR][1000 genomes]
rs602204	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs612037	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61799500	0.83[ASN][1000 genomes]
rs622608	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624131	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs627779	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs637646	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6541349	0.82[ASN][1000 genomes]
rs6541401	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541404	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6658257	0.82[ASN][1000 genomes]
rs6680022	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6680107	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6682670	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6688230	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6694508	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6703310	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs687394	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693737	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72959220	0.83[ASN][1000 genomes]
rs7417952	0.86[EUR][1000 genomes]
rs7418101	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7512911	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7513705	0.88[EUR][1000 genomes]
rs7517363	0.82[ASN][1000 genomes]
rs7524964	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7525248	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7526112	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532195	0.84[EUR][1000 genomes]
rs7535628	0.87[EUR][1000 genomes]
rs7537403	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539307	0.87[EUR][1000 genomes]
rs7540025	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541304	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541687	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7547244	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7551485	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7553465	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7553916	0.83[ASN][1000 genomes]
rs797661	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs797666	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797668	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797671	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797672	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs797676	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs797680	0.80[AMR][1000 genomes]
rs797681	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942196	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9432453	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9432459	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9432465	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9432681	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9660390	0.85[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs682514	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs682514	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs682514	RP4-717I23.3	cis	Artery Aorta	GTEx
rs682514	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs682514	RP4-717I23.3	cis	Whole Blood	GTEx
rs682514	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs682514	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs682514	RP4-717I23.3	cis	Artery Tibial	GTEx
rs682514	RP4-717I23.3	cis	Thyroid	GTEx
rs682514	DR1	cis	multi-tissue	Pritchard
rs682514	DR1	cis	Adipose Subcutaneous	GTEx
rs682514	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs682514	CCDC18	cis	Nerve Tibial	GTEx
rs682514	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs682514	RP4-717I23.3	cis	lung	GTEx
rs682514	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs682514	RP4-717I23.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:96 , 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	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
6	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
8	chr1:93706400-93727000	Weak transcription	K562	blood
9	chr1:93707000-93727400	Weak transcription	Liver	Liver
10	chr1:93708800-93720200	Weak transcription	NHLF	lung
11	chr1:93709000-93719800	Weak transcription	HSMM	muscle
12	chr1:93709000-93720800	Weak transcription	Osteobl	bone
13	chr1:93709000-93724200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:93709000-93726400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:93709000-93727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:93709000-93728200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:93709000-93728200	Weak transcription	HMEC	breast
18	chr1:93709200-93727400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:93709400-93727600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:93709600-93720200	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:93709600-93725000	Weak transcription	HepG2	liver
22	chr1:93709600-93725600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:93709600-93727000	Weak transcription	NHEK	skin
24	chr1:93709800-93727000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:93709800-93727000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:93710000-93721600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:93710000-93727000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:93710200-93721800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:93710200-93722200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:93710200-93724200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:93710200-93727000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:93710600-93724400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:93710800-93720000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:93711000-93719800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:93711600-93727000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:93713200-93727000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:93713400-93721600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:93715200-93720800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:93716200-93728400	Weak transcription	Pancreas	Pancrea
40	chr1:93716800-93727600	Weak transcription	Fetal Kidney	kidney
41	chr1:93717200-93726200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:93717800-93725600	Strong transcription	Dnd41	blood
43	chr1:93717800-93727800	Weak transcription	Ovary	ovary
44	chr1:93718200-93727000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:93718400-93727000	Weak transcription	Fetal Lung	lung
46	chr1:93718400-93727000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:93718600-93720600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:93718600-93720800	Weak transcription	Fetal Thymus	thymus
49	chr1:93718600-93727000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:93718600-93727800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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