Variant report

Variant	rs10490039
Chromosome Location	chr2:72429239-72429240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72420139..72423033-chr2:72428492..72430569,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1002415	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171231	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490040	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13339845	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389007	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007906	1.00[ASN][1000 genomes]
rs17007927	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007929	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007933	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007934	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007937	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192012	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813510	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994075	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152907	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57013742	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58032693	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58173605	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58339219	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59269913	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61391258	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61450122	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147574	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147580	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147581	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147586	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147587	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147588	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147590	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147598	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147600	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147601	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147622	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147623	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147624	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147625	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147627	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147630	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147631	1.00[ASN][1000 genomes]
rs62147637	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147740	1.00[ASN][1000 genomes]
rs62150087	1.00[ASN][1000 genomes]
rs62150096	1.00[ASN][1000 genomes]
rs62150097	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150118	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150119	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150120	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150123	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546745	0.88[CEU][hapmap]
rs6546747	0.88[CEU][hapmap]
rs6705261	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705347	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707549	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748698	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910329	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910330	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910350	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583202	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs7596302	0.87[CEU][hapmap]

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
rs10490039	IRX3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72412800-72429800	Weak transcription	Right Ventricle	heart
2	chr2:72412800-72431000	Weak transcription	Left Ventricle	heart
3	chr2:72415400-72430800	Weak transcription	Placenta	Placenta
4	chr2:72419000-72430800	Weak transcription	Small Intestine	intestine
5	chr2:72422200-72430400	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:72424600-72429600	Weak transcription	Right Atrium	heart
7	chr2:72426200-72430800	Weak transcription	HepG2	liver
8	chr2:72426200-72431000	Weak transcription	Gastric	stomach
9	chr2:72426200-72431400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:72426200-72431400	Weak transcription	NHLF	lung
11	chr2:72426600-72430600	Weak transcription	Brain Anterior Caudate	brain
12	chr2:72426600-72430800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:72426600-72430800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:72426600-72430800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:72426600-72430800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:72426600-72430800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:72426600-72430800	Weak transcription	NHEK	skin
18	chr2:72426600-72432000	Weak transcription	HSMM	muscle
19	chr2:72426800-72430600	Weak transcription	HMEC	breast
20	chr2:72426800-72430800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:72426800-72430800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:72426800-72430800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:72426800-72430800	Weak transcription	Stomach Mucosa	stomach
24	chr2:72426800-72437600	Weak transcription	NH-A	brain
25	chr2:72427000-72431000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:72427000-72431800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:72427000-72432000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:72427000-72432000	Weak transcription	Osteobl	bone
29	chr2:72427000-72432200	Weak transcription	NHDF-Ad	bronchial
30	chr2:72427200-72430800	Weak transcription	Esophagus	oesophagus
31	chr2:72428800-72431400	Enhancers	A549	lung
32	chr2:72429000-72433200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:72429200-72429800	Enhancers	Brain Substantia Nigra	brain
34	chr2:72429200-72433600	Enhancers	Fetal Intestine Large	intestine

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