Variant report

Variant	rs29481
Chromosome Location	chr7:41186832-41186833
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10227446	0.89[ASN][1000 genomes]
rs10227663	0.88[ASN][1000 genomes]
rs10242681	0.85[CEU][hapmap]
rs10256962	0.89[ASN][1000 genomes]
rs10258940	0.94[ASN][1000 genomes]
rs10274211	0.94[ASN][1000 genomes]
rs10279346	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10755853	0.87[ASN][1000 genomes]
rs10755854	0.87[ASN][1000 genomes]
rs12670349	0.88[CEU][hapmap];0.84[ASN][1000 genomes]
rs12701863	0.85[ASN][1000 genomes]
rs12701864	0.86[ASN][1000 genomes]
rs12701875	0.85[CEU][hapmap]
rs13222193	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs13222281	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs13234888	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs13246656	0.82[ASN][1000 genomes]
rs1859692	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1859693	0.93[ASN][1000 genomes]
rs1859694	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108155	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2108156	0.93[ASN][1000 genomes]
rs2108157	0.87[ASN][1000 genomes]
rs2190329	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2330001	0.87[ASN][1000 genomes]
rs28176	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28880	0.94[ASN][1000 genomes]
rs29476	0.94[ASN][1000 genomes]
rs29477	0.94[ASN][1000 genomes]
rs29478	0.94[ASN][1000 genomes]
rs29479	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29480	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29482	0.94[ASN][1000 genomes]
rs29484	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs29492	0.93[EUR][1000 genomes]
rs29503	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29508	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs29509	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29511	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29516	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs29517	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs29519	0.90[EUR][1000 genomes]
rs29522	0.90[EUR][1000 genomes]
rs29523	0.86[EUR][1000 genomes]
rs29524	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4720399	0.94[ASN][1000 genomes]
rs4724027	0.95[CHB][hapmap]
rs4724028	0.87[ASN][1000 genomes]
rs4724029	0.91[ASN][1000 genomes]
rs6463004	0.87[ASN][1000 genomes]
rs6463005	0.88[ASN][1000 genomes]
rs6463006	0.91[ASN][1000 genomes]
rs6463007	0.91[ASN][1000 genomes]
rs6463008	0.86[ASN][1000 genomes]
rs6945256	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6945901	0.91[ASN][1000 genomes]
rs6946898	0.91[ASN][1000 genomes]
rs6947021	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958423	0.91[ASN][1000 genomes]
rs6958959	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6967416	0.87[ASN][1000 genomes]
rs6970635	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6971196	0.85[ASN][1000 genomes]
rs6971616	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6975061	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6978132	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7790556	0.89[ASN][1000 genomes]
rs7796964	0.85[CEU][hapmap]
rs7799191	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7805795	0.91[ASN][1000 genomes]
rs7809083	0.84[ASN][1000 genomes]
rs9632614	0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs29481	NPC1L1	cis	parietal	SCAN
rs29481	MYL7	cis	parietal	SCAN

Chromatin state (count:14 , 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	chr7:41185200-41187800	Enhancers	NHEK	skin
4	chr7:41185200-41189600	Enhancers	HMEC	breast
5	chr7:41185400-41187600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:41185600-41189000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:41185800-41187200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:41185800-41187200	Weak transcription	NHDF-Ad	bronchial
9	chr7:41185800-41188000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:41186200-41187400	Weak transcription	Fetal Stomach	stomach
11	chr7:41186600-41189200	Enhancers	Hela-S3	cervix
12	chr7:41186600-41189400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:41186800-41189000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:41186800-41189000	Enhancers	Osteobl	bone

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