Variant report

Variant	rs58173605
Chromosome Location	chr2:72439951-72439952
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1002415	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171231	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490039	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13339845	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389007	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007906	1.00[ASN][1000 genomes]
rs17007927	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007929	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007933	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007934	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007937	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192012	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813510	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994075	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152907	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57013742	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58032693	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58339219	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59269913	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61391258	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61450122	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147574	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147580	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147581	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147586	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147587	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147588	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147590	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147598	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147600	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147601	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147622	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147623	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147624	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147625	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147627	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147630	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147631	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147637	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150087	1.00[ASN][1000 genomes]
rs62150096	1.00[ASN][1000 genomes]
rs62150097	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150118	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150119	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150120	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150123	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705261	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705347	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707549	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748698	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910330	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910350	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583202	1.00[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	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58173605	IRX3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72432800-72441600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:72432800-72456600	Weak transcription	Psoas Muscle	Psoas
3	chr2:72433000-72441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:72433000-72460600	Weak transcription	Pancreas	Pancrea
5	chr2:72433200-72440200	Weak transcription	Left Ventricle	heart
6	chr2:72433200-72442200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:72433200-72450000	Weak transcription	Brain Angular Gyrus	brain
8	chr2:72433200-72450000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:72433200-72466000	Weak transcription	Right Ventricle	heart
10	chr2:72433200-72468600	Weak transcription	Right Atrium	heart
11	chr2:72433400-72450200	Weak transcription	Brain Anterior Caudate	brain
12	chr2:72433600-72442000	Weak transcription	Fetal Stomach	stomach
13	chr2:72437800-72440200	Enhancers	Duodenum Mucosa	Duodenum
14	chr2:72437800-72440400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:72437800-72440600	Enhancers	Osteobl	bone
16	chr2:72438000-72440200	Weak transcription	Colonic Mucosa	Colon
17	chr2:72438200-72442200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:72438200-72446400	Weak transcription	Fetal Heart	heart
19	chr2:72438400-72440200	Weak transcription	Esophagus	oesophagus
20	chr2:72438400-72449800	Weak transcription	HMEC	breast
21	chr2:72438600-72440600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:72439000-72441000	Weak transcription	A549	lung
23	chr2:72439200-72440200	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:72439400-72440200	Enhancers	NHDF-Ad	bronchial
25	chr2:72439400-72441200	Weak transcription	Small Intestine	intestine
26	chr2:72439400-72441600	Weak transcription	NH-A	brain
27	chr2:72439600-72441800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:72439600-72441800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:72439800-72440400	Enhancers	Sigmoid Colon	Sigmoid Colon

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