Variant report

Variant	rs7538392
Chromosome Location	chr1:222222851-222222852
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222222029..222224005-chr1:222224328..222226872,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11118920	0.89[EUR][1000 genomes]
rs11118930	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11118931	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12031848	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12139468	1.00[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1339870	0.90[EUR][1000 genomes]
rs1339873	0.86[ASN][1000 genomes]
rs1416896	0.89[EUR][1000 genomes]
rs1470233	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2053510	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2053511	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2053512	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2378499	0.92[EUR][1000 genomes]
rs2584314	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2584315	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2584316	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2584317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2584318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2584319	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2584320	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2584321	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584322	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2584323	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2584324	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2584329	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2790744	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2790745	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2790746	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2790747	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2790748	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800848	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2800849	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800861	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800865	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2800866	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800867	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3014719	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56120858	0.89[EUR][1000 genomes]
rs61823931	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6604697	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6677832	0.89[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	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7538392	IARS2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222217400-222223800	Weak transcription	Aorta	Aorta
2	chr1:222218000-222227800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:222218800-222223000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:222220600-222223200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:222220800-222223000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:222220800-222223000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:222221200-222223000	Enhancers	GM12878-XiMat	blood
8	chr1:222221400-222223000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:222222200-222223000	Enhancers	Rectal Smooth Muscle	rectum
10	chr1:222222400-222223400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:222222400-222229200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:222222600-222228200	Weak transcription	Fetal Brain Male	brain
13	chr1:222222800-222224000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:222222800-222224000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:222222800-222224200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:222222800-222224600	Weak transcription	HMEC	breast
17	chr1:222222800-222227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:222222800-222227800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:222222800-222228600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:222222800-222232200	Weak transcription	HSMM	muscle

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