Variant report

Variant	rs3087585
Chromosome Location	chr1:58971831-58971832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TACSTD2-4	chr1:58971732-58971871	NONHSAT003504

Extended variants
information (count: 123 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10458559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10489815	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10789063	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10789064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10789065	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10789066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10789067	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs10889099	1.00[ASN][1000 genomes]
rs10889100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10889101	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1109895	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1109896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207236	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11207237	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11207238	0.88[ASN][1000 genomes]
rs11207239	0.88[ASN][1000 genomes]
rs11207240	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11207245	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207246	1.00[ASN][1000 genomes]
rs11207247	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11207248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11207250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207253	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207254	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207255	0.94[ASN][1000 genomes]
rs11207260	0.82[ASN][1000 genomes]
rs11207262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1121422	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11581395	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11589214	0.82[ASN][1000 genomes]
rs11589236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11590757	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11590785	1.00[ASN][1000 genomes]
rs12030713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12058651	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12067296	0.82[ASN][1000 genomes]
rs12067565	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12068196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12068201	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12068391	0.82[ASN][1000 genomes]
rs12068457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12070503	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12072998	1.00[ASN][1000 genomes]
rs12077340	0.82[ASN][1000 genomes]
rs12077766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12080357	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12088149	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12088905	0.88[ASN][1000 genomes]
rs12097882	0.82[ASN][1000 genomes]
rs12118488	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12121129	0.88[ASN][1000 genomes]
rs12124662	1.00[ASW][hapmap];0.95[CEU][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12125391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133823	1.00[ASN][1000 genomes]
rs12139475	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12141238	1.00[ASN][1000 genomes]
rs12142098	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12144759	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17117742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17117873	0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17372425	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17461345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1775002	0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs2087799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs232826	0.95[CEU][hapmap]
rs232848	0.82[ASN][1000 genomes]
rs232849	0.82[ASN][1000 genomes]
rs2406784	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28529311	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs338225	0.93[MEX][hapmap]
rs338228	0.84[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs34023272	0.82[ASN][1000 genomes]
rs34135541	0.82[ASN][1000 genomes]
rs3893156	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs486463	0.95[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs4912195	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56049576	0.94[ASN][1000 genomes]
rs56087605	0.88[ASN][1000 genomes]
rs56138615	0.88[ASN][1000 genomes]
rs562166	0.82[ASN][1000 genomes]
rs584579	0.82[ASN][1000 genomes]
rs59607787	0.82[ASN][1000 genomes]
rs602579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[ASN][1000 genomes]
rs603031	0.82[ASN][1000 genomes]
rs60490291	1.00[ASN][1000 genomes]
rs60726128	0.94[ASN][1000 genomes]
rs620342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs627218	0.82[ASN][1000 genomes]
rs6587818	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587819	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs659061	0.95[CEU][hapmap]
rs6656025	0.93[MEX][hapmap];0.80[TSI][hapmap]
rs6661832	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6666138	1.00[JPT][hapmap]
rs6666304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6667614	0.86[MEX][hapmap];0.80[TSI][hapmap]
rs6679808	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6687324	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[GIH][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6690139	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6704300	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67443104	0.82[ASN][1000 genomes]
rs67639631	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67805407	0.82[ASN][1000 genomes]
rs68192782	0.82[ASN][1000 genomes]
rs72672216	1.00[ASN][1000 genomes]
rs7355165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355166	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515056	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7517424	0.81[EUR][1000 genomes]
rs7520008	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7536230	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7536867	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7546900	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547036	0.95[CEU][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs7554278	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs905567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3087585	OMA1	cis	parietal	SCAN
rs3087585	MYSM1	cis	parietal	SCAN
rs3087585	ENSG00000162600	cis	multi-tissue	Pritchard
rs3087585	OMA1	cis	lymphoblastoid	seeQTL
rs3087585	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs3087585	TACSTD2	cis	Thyroid	GTEx
rs3087585	DAB1	cis	parietal	SCAN
rs3087585	DAB1	cis	cerebellum	SCAN
rs3087585	TACSTD2	cis	Whole Blood	GTEx
rs3087585	OMA1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58918400-58974000	Weak transcription	Spleen	Spleen
2	chr1:58931000-58977000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:58931600-58974000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:58932600-58974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:58932600-58977000	Weak transcription	HSMMtube	muscle
7	chr1:58933800-58984800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:58934600-58974000	Weak transcription	Right Ventricle	heart
9	chr1:58934800-58976600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:58934800-58994000	Weak transcription	HSMM	muscle
11	chr1:58935000-58974000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:58942000-58974200	Weak transcription	Brain Substantia Nigra	brain
13	chr1:58942200-58974200	Weak transcription	Fetal Thymus	thymus
14	chr1:58944600-58976000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:58945800-58974200	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:58946200-58974000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:58946200-58977000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:58946200-58979600	Weak transcription	GM12878-XiMat	blood
19	chr1:58946400-58973800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:58946400-58993800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:58946600-58977000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:58947600-58977000	Weak transcription	Brain Angular Gyrus	brain
23	chr1:58948400-58977000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:58950200-58976600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:58952800-58977200	Weak transcription	Small Intestine	intestine
26	chr1:58953000-58974000	Weak transcription	Fetal Lung	lung
27	chr1:58953200-58986000	Weak transcription	Colonic Mucosa	Colon
28	chr1:58953600-58999200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:58955000-58974000	Weak transcription	Esophagus	oesophagus
30	chr1:58955000-58974000	Weak transcription	Pancreas	Pancrea
31	chr1:58955000-58974000	Weak transcription	Thymus	Thymus
32	chr1:58955000-58976600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:58955000-58976800	Weak transcription	Fetal Kidney	kidney
34	chr1:58955000-58986400	Weak transcription	Gastric	stomach
35	chr1:58955000-58988200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:58955200-58974000	Weak transcription	Aorta	Aorta
37	chr1:58960800-58976600	Weak transcription	Brain Anterior Caudate	brain
38	chr1:58961600-58974200	Weak transcription	Fetal Stomach	stomach
39	chr1:58963400-58974200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:58963800-58974000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:58963800-58999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:58964200-58978600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:58964800-58986400	Weak transcription	K562	blood
44	chr1:58965600-58972000	Strong transcription	Primary B cells from cord blood	blood
45	chr1:58966400-58974000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:58966400-58976800	Weak transcription	NHEK	skin
47	chr1:58966600-59010600	Weak transcription	Placenta	Placenta
48	chr1:58967000-58972000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:58967400-58972200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr1:58967600-59010600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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