Variant report

Variant	rs10889098
Chromosome Location	chr1:58973464-58973465
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10489815	0.93[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10789063	0.98[ASN][1000 genomes]
rs10789067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10889099	0.81[EUR][1000 genomes]
rs1114660	1.00[ASN][1000 genomes]
rs11207236	0.96[ASN][1000 genomes]
rs11207237	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11207238	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11207239	0.89[EUR][1000 genomes]
rs11207240	0.96[ASN][1000 genomes]
rs11207246	0.94[EUR][1000 genomes]
rs11207247	0.87[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11207248	0.87[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11207255	0.82[AFR][1000 genomes]
rs11207262	0.87[CEU][hapmap];0.95[YRI][hapmap]
rs1121422	1.00[ASN][1000 genomes]
rs11581395	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11589236	0.85[CEU][hapmap]
rs11590757	0.93[CEU][hapmap];0.94[YRI][hapmap]
rs11590785	0.81[EUR][1000 genomes]
rs12030713	0.87[ASN][1000 genomes]
rs12058651	0.87[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12067565	0.83[CEU][hapmap]
rs12068201	0.87[CEU][hapmap]
rs12068457	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs12070503	0.87[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12072998	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12080357	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs12088149	0.96[ASN][1000 genomes]
rs12088905	0.88[EUR][1000 genomes]
rs12118488	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs12121129	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12124662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12133823	0.94[EUR][1000 genomes]
rs12139475	0.86[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs12141238	0.94[EUR][1000 genomes]
rs12144759	0.93[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1388981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17117742	0.86[CEU][hapmap]
rs17117873	0.93[CEU][hapmap]
rs1775002	0.82[ASN][1000 genomes]
rs232826	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs28529311	0.96[ASN][1000 genomes]
rs338224	0.96[ASN][1000 genomes]
rs338225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3893156	0.85[CEU][hapmap]
rs486463	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4912195	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4912344	0.87[ASN][1000 genomes]
rs56049576	0.82[AFR][1000 genomes]
rs56087605	0.89[EUR][1000 genomes]
rs56138615	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60490291	0.93[EUR][1000 genomes]
rs6587818	1.00[ASN][1000 genomes]
rs6587819	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6587821	0.87[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587828	0.87[ASN][1000 genomes]
rs659061	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6656025	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6667614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6667703	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs6679808	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs6687324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6690139	0.93[CEU][hapmap]
rs6704300	0.87[CEU][hapmap]
rs67639631	0.87[ASN][1000 genomes]
rs7515056	0.81[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7517424	0.86[ASN][1000 genomes]
rs7520008	0.87[ASN][1000 genomes]
rs7536230	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7536867	0.87[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7544032	0.87[ASN][1000 genomes]
rs7547036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7554278	0.96[ASN][1000 genomes]
rs9660901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10889098	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs10889098	TACSTD2	cis	Whole Blood	GTEx

Chromatin state (count:91 , 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	chr1:58966400-58974000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:58966400-58976800	Weak transcription	NHEK	skin
46	chr1:58966600-59010600	Weak transcription	Placenta	Placenta
47	chr1:58967600-59010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:58968200-58986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:58968400-58984600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:58969200-58977000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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