Variant report

Variant	rs28880
Chromosome Location	chr7:41185851-41185852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10227446	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10227663	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10256962	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10258940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10274211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279346	0.87[ASN][1000 genomes]
rs10755853	0.83[ASN][1000 genomes]
rs10755854	0.84[ASN][1000 genomes]
rs12670349	0.81[ASN][1000 genomes]
rs12701863	0.82[ASN][1000 genomes]
rs12701864	0.82[ASN][1000 genomes]
rs13222193	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs13222281	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs13234888	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs13246656	0.88[ASN][1000 genomes]
rs1859692	0.92[ASN][1000 genomes]
rs1859693	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859694	0.94[ASN][1000 genomes]
rs2108155	0.86[ASN][1000 genomes]
rs2108156	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108157	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2190329	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2330001	0.83[ASN][1000 genomes]
rs28238	0.92[EUR][1000 genomes]
rs28314	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29476	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29479	0.95[ASN][1000 genomes]
rs29480	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs29481	0.94[ASN][1000 genomes]
rs29482	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29483	0.86[EUR][1000 genomes]
rs29485	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs29486	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs29488	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs29489	0.93[EUR][1000 genomes]
rs29490	0.93[EUR][1000 genomes]
rs29492	0.90[AFR][1000 genomes]
rs29493	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29494	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs29495	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29496	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29497	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29498	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29499	0.92[EUR][1000 genomes]
rs29500	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29501	0.92[EUR][1000 genomes]
rs29502	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29503	0.93[ASN][1000 genomes]
rs29504	0.91[EUR][1000 genomes]
rs29505	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29506	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29512	0.91[EUR][1000 genomes]
rs29513	0.91[EUR][1000 genomes]
rs29514	0.85[EUR][1000 genomes]
rs29515	0.91[EUR][1000 genomes]
rs29516	0.88[ASN][1000 genomes]
rs29517	0.88[ASN][1000 genomes]
rs29518	0.91[EUR][1000 genomes]
rs29521	0.90[EUR][1000 genomes]
rs29525	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs29526	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4720399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724027	0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs4724028	0.83[ASN][1000 genomes]
rs4724029	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6463004	0.93[ASN][1000 genomes]
rs6463005	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6463006	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6463007	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6463008	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6945256	0.92[ASN][1000 genomes]
rs6945901	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6946898	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6947021	0.92[ASN][1000 genomes]
rs6951425	0.96[CEU][hapmap]
rs6958423	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6958959	0.92[ASN][1000 genomes]
rs6967416	0.83[ASN][1000 genomes]
rs6970635	0.86[ASN][1000 genomes]
rs6971196	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6971616	0.89[ASN][1000 genomes]
rs6975061	0.91[ASN][1000 genomes]
rs6978132	0.92[ASN][1000 genomes]
rs7790556	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7799191	0.86[ASN][1000 genomes]
rs7805795	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7809083	0.81[ASN][1000 genomes]
rs9632614	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034605	chr7:41096638-41222426	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv887989	chr7:41125447-41337044	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1028983	chr7:41165668-41635954	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28880	MYO1G	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41174400-41187800	Weak transcription	NHLF	lung
2	chr7:41183600-41187200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:41183800-41186600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:41184000-41186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:41184000-41186800	Weak transcription	Osteobl	bone
6	chr7:41185200-41186200	Enhancers	Fetal Stomach	stomach
7	chr7:41185200-41187800	Enhancers	NHEK	skin
8	chr7:41185200-41189600	Enhancers	HMEC	breast
9	chr7:41185400-41187600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:41185600-41189000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:41185800-41187200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:41185800-41187200	Weak transcription	NHDF-Ad	bronchial
13	chr7:41185800-41188000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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