Variant report

Variant	rs62147574
Chromosome Location	chr2:72437602-72437603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72432812..72434707-chr2:72436307..72438652,2	MCF-7	breast:
2	chr2:72431398..72433535-chr2:72436487..72438674,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

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	0.81[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	0.91[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	0.90[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]
rs58173605	0.83[AFR][1000 genomes];1.00[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	0.93[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]
rs62147580	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147581	0.98[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]
rs62147740	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	0.92[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	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748698	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910329	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910330	0.89[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
rs62147574	IRX3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72432800-72437800	Weak transcription	Osteobl	bone
2	chr2:72432800-72438400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:72432800-72438400	Weak transcription	NHDF-Ad	bronchial
4	chr2:72432800-72441600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:72432800-72456600	Weak transcription	Psoas Muscle	Psoas
6	chr2:72433000-72441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:72433000-72460600	Weak transcription	Pancreas	Pancrea
8	chr2:72433200-72437800	Weak transcription	Ovary	ovary
9	chr2:72433200-72438600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:72433200-72440200	Weak transcription	Left Ventricle	heart
11	chr2:72433200-72442200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:72433200-72450000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:72433200-72450000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:72433200-72466000	Weak transcription	Right Ventricle	heart
15	chr2:72433200-72468600	Weak transcription	Right Atrium	heart
16	chr2:72433400-72437800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:72433400-72450200	Weak transcription	Brain Anterior Caudate	brain
18	chr2:72433600-72437800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:72433600-72437800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:72433600-72439000	Weak transcription	Small Intestine	intestine
21	chr2:72433600-72442000	Weak transcription	Fetal Stomach	stomach
22	chr2:72436600-72439000	Enhancers	A549	lung
23	chr2:72437400-72438200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:72437400-72438200	Enhancers	Fetal Heart	heart
25	chr2:72437400-72439400	Enhancers	NHEK	skin
26	chr2:72437400-72439800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr2:72437600-72437800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:72437600-72438000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:72437600-72438000	Enhancers	Colonic Mucosa	Colon
30	chr2:72437600-72438400	Enhancers	Esophagus	oesophagus
31	chr2:72437600-72438800	Enhancers	Gastric	stomach
32	chr2:72437600-72438800	Enhancers	NH-A	brain
33	chr2:72437600-72439000	Enhancers	Stomach Mucosa	stomach
34	chr2:72437600-72439400	Enhancers	Fetal Intestine Large	intestine
35	chr2:72437600-72439400	Enhancers	Fetal Intestine Small	intestine
36	chr2:72437600-72439800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links