Variant report

Variant	rs62287066
Chromosome Location	chr3:195022006-195022007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10439946	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10439947	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10439948	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10439949	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11706218	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11709417	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11715202	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11718226	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12054139	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12054333	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12054406	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12630009	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12636736	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13316914	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13317705	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13325966	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1538768	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1826584	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1994880	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1994881	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2000051	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2000052	0.86[EUR][1000 genomes]
rs2066154	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275518	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2410804	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4461369	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4677668	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4677669	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4677826	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677827	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4677829	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4677832	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677833	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4677837	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677838	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677842	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4677843	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57124286	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57760978	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58178384	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59004692	0.81[ASN][1000 genomes]
rs59563484	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60042817	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60100329	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60177727	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62285259	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62287061	0.80[EUR][1000 genomes]
rs62287069	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62287106	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62287107	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62287108	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62287109	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62287111	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62287119	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62288360	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62288364	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62288365	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62288367	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62288369	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62288441	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62288442	0.81[ASN][1000 genomes]
rs6437373	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6437375	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6437471	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6763335	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771771	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6778652	0.81[AMR][1000 genomes]
rs6788868	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6791563	0.80[AMR][1000 genomes]
rs6794216	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6800221	0.81[ASN][1000 genomes]
rs6801007	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6801315	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6803763	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806850	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs716898	0.81[EUR][1000 genomes]
rs73208931	0.81[ASN][1000 genomes]
rs7430205	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611090	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7616598	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617936	0.81[EUR][1000 genomes]
rs7618499	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621133	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7622180	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7627054	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7632534	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7635906	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7636824	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7639146	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7641810	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7650623	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7652612	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653406	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9790153	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809730	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814344	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9817672	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9821765	0.81[ASN][1000 genomes]
rs9826999	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9836665	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9844354	0.81[EUR][1000 genomes]
rs9846555	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9848201	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9848473	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854941	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9855453	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9859902	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9862710	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870236	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9876967	0.81[ASN][1000 genomes]
rs9879305	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	73 gene(s)	inside rSNPs	diseases
3	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
4	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
10	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
11	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
12	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62287066	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx
rs62287066	XXYLT1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
2	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
3	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
4	chr3:194993000-195038600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:194993000-195039200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:194993000-195039600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:194993000-195050400	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
9	chr3:194995000-195039800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:194995400-195040000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:194996200-195032200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:194996400-195033800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr3:194997200-195027400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:194999200-195029400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:195002200-195028200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:195002600-195024000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:195002600-195024800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:195002600-195027400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:195003600-195028600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:195004000-195039600	Weak transcription	Pancreas	Pancrea
21	chr3:195004000-195066600	Weak transcription	Small Intestine	intestine
22	chr3:195004200-195039600	Weak transcription	Gastric	stomach
23	chr3:195005200-195039600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:195005600-195022800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:195007800-195029600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:195008000-195024400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:195008000-195025400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:195008000-195039800	Weak transcription	NH-A	brain
29	chr3:195009200-195025400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:195009600-195023800	Weak transcription	Esophagus	oesophagus
31	chr3:195010000-195039000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:195010000-195039600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:195010000-195039800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:195010000-195039800	Weak transcription	Brain Substantia Nigra	brain
35	chr3:195010000-195061000	Weak transcription	Fetal Kidney	kidney
36	chr3:195010000-195076400	Weak transcription	Brain Angular Gyrus	brain
37	chr3:195010400-195022600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:195011400-195022400	Weak transcription	NHEK	skin
39	chr3:195013200-195024200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:195013200-195028800	Weak transcription	NHDF-Ad	bronchial
41	chr3:195013200-195039400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:195014200-195040800	Weak transcription	Hela-S3	cervix
43	chr3:195014400-195022200	Weak transcription	Brain Anterior Caudate	brain
44	chr3:195014400-195024200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:195014600-195022400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:195014800-195025400	Weak transcription	Lung	lung
47	chr3:195015600-195024800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:195015600-195026800	Strong transcription	Adipose Nuclei	Adipose
49	chr3:195016000-195039600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:195016200-195022200	Weak transcription	HMEC	breast

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