Variant report

Variant	rs13339845
Chromosome Location	chr2:72419864-72419865
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	chr2:72417923..72420576-chr2:72426721..72428374,2	MCF-7	breast:

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]
rs10490039	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490040	1.00[CEU][hapmap];0.92[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[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007929	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007933	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007934	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007937	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192012	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813510	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994075	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152907	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57013742	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58032693	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58173605	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58339219	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59269913	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61391258	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61450122	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147574	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147580	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147581	0.89[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	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150118	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150119	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150120	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150123	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546745	0.88[CEU][hapmap]
rs6546747	0.88[CEU][hapmap]
rs6705261	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705347	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707549	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748698	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910329	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910330	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910350	0.92[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
rs13339845	IRX3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72406400-72425800	Weak transcription	Brain Anterior Caudate	brain
2	chr2:72407200-72425200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:72407800-72424600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:72409600-72426000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:72410600-72420000	Weak transcription	A549	lung
6	chr2:72412800-72421600	Weak transcription	Gastric	stomach
7	chr2:72412800-72425400	Weak transcription	Stomach Mucosa	stomach
8	chr2:72412800-72429800	Weak transcription	Right Ventricle	heart
9	chr2:72412800-72431000	Weak transcription	Left Ventricle	heart
10	chr2:72415200-72426000	Weak transcription	NHEK	skin
11	chr2:72415400-72424400	Weak transcription	Aorta	Aorta
12	chr2:72415400-72426000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:72415400-72430800	Weak transcription	Placenta	Placenta
14	chr2:72419000-72420200	Weak transcription	Fetal Lung	lung
15	chr2:72419000-72430800	Weak transcription	Small Intestine	intestine
16	chr2:72419600-72429200	Weak transcription	Brain Substantia Nigra	brain
17	chr2:72419800-72420000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:72419800-72420000	Enhancers	Brain Cingulate Gyrus	brain

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