Variant report

Variant	rs2589510
Chromosome Location	chr4:86927858-86927859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs189395	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs189396	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2043647	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2136782	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2164538	1.00[CEU][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2575681	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2575682	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2589505	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2665869	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2665876	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346469	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346470	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs346472	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346473	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346476	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346477	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346482	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346483	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs346486	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346487	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346489	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346490	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346491	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346493	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346494	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346495	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346496	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346499	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs346500	0.90[MEX][hapmap]
rs346501	0.90[MEX][hapmap]
rs62305518	0.95[AMR][1000 genomes];0.97[EUR][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	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2589510	THAP9	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
2	chr4:86916800-86929400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:86916800-86935800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:86916800-86985400	Weak transcription	Ovary	ovary
5	chr4:86917000-86929000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:86917000-86931800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:86917000-86931800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:86917000-86931800	Weak transcription	Osteobl	bone
9	chr4:86917000-86932000	Weak transcription	NHLF	lung
10	chr4:86917000-86932400	Weak transcription	Fetal Lung	lung
11	chr4:86917000-86932400	Weak transcription	Right Ventricle	heart
12	chr4:86917000-86933800	Weak transcription	Gastric	stomach
13	chr4:86917000-86933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:86917000-86935200	Weak transcription	Left Ventricle	heart
15	chr4:86917000-86935800	Weak transcription	Spleen	Spleen
16	chr4:86917000-86954000	Weak transcription	Pancreas	Pancrea
17	chr4:86917200-86932000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:86917400-86940400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:86917800-86931600	Weak transcription	NHDF-Ad	bronchial
20	chr4:86918000-86931800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr4:86919400-86941200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:86920200-86933800	Weak transcription	Aorta	Aorta
23	chr4:86920800-86928600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:86921200-86928400	Strong transcription	HUVEC	blood vessel
25	chr4:86921800-86932200	Weak transcription	Fetal Heart	heart
26	chr4:86922800-86935200	Weak transcription	Right Atrium	heart
27	chr4:86923400-86931800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:86924200-86928600	Strong transcription	Fetal Muscle Leg	muscle
29	chr4:86925400-86937200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:86925600-86931800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:86925600-86932400	Weak transcription	HSMM	muscle
32	chr4:86925600-86935000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:86925600-86935200	Weak transcription	Adipose Nuclei	Adipose
34	chr4:86925600-86935600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:86925600-86937400	Weak transcription	Fetal Kidney	kidney
36	chr4:86926400-86928600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr4:86926600-86928200	Strong transcription	HSMMtube	muscle
38	chr4:86927400-86935400	Weak transcription	Primary B cells from cord blood	blood
39	chr4:86927800-86928400	Strong transcription	Fetal Stomach	stomach
40	chr4:86927800-86929400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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