Variant report

Variant	rs40457
Chromosome Location	chr8:90823687-90823688
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	chr8:90819524..90821279-chr8:90821317..90823717,2	MCF-7	breast:
2	chr8:90812604..90815452-chr8:90823390..90825028,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1003843	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap]
rs10112852	0.85[CHB][hapmap]
rs11989430	0.84[ASN][1000 genomes]
rs13280951	0.90[ASN][1000 genomes]
rs218907	0.85[CHB][hapmap]
rs218908	0.85[CHB][hapmap]
rs218913	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs218929	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs2338882	0.90[ASN][1000 genomes]
rs28144	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28405481	0.84[ASN][1000 genomes]
rs28461337	0.90[ASN][1000 genomes]
rs2975240	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368812	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs369771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs370282	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs374957	0.95[GIH][hapmap]
rs376110	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs383592	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs394108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39501	0.82[CEU][hapmap]
rs39502	0.82[CEU][hapmap]
rs39503	0.83[MEX][hapmap]
rs39506	0.83[MEX][hapmap]
rs39509	0.85[CEU][hapmap]
rs39515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39516	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39519	0.95[GIH][hapmap];0.87[YRI][hapmap]
rs39762	0.82[CEU][hapmap]
rs39767	0.92[EUR][1000 genomes]
rs39768	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39769	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39771	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs402434	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40247	0.81[CEU][hapmap]
rs40381	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40382	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40453	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs40458	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40547	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40636	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40637	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40638	0.92[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40639	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs410663	0.87[MEX][hapmap]
rs411279	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs416324	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs421411	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422559	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42345	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42346	0.92[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs42479	0.82[CEU][hapmap]
rs43133	0.82[CEU][hapmap]
rs43135	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs43136	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs43226	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs43227	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs43228	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs43229	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs435600	0.81[EUR][1000 genomes]
rs438485	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs441548	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs445172	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445675	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447611	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447618	0.87[MEX][hapmap]
rs452694	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs453266	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs454561	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs51331	0.85[CEU][hapmap]
rs62530862	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv972243	chr8:90823430-90834708	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	nsv520356	chr8:90823687-90857989	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Leprosy	20018961	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs40457	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx
rs40457	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs40457	RIPK2	Cis_1M	lymphoblastoid	RTeQTL
rs40457	CALB1	cis	cerebellum	SCAN
rs40457	RIPK2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90783800-90829000	Weak transcription	Aorta	Aorta
2	chr8:90814000-90824600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr8:90817400-90825200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:90818000-90824600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr8:90818600-90824800	Weak transcription	A549	lung
6	chr8:90822800-90826600	Enhancers	Osteobl	bone
7	chr8:90823000-90824800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr8:90823200-90824600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr8:90823400-90824000	Enhancers	NHDF-Ad	bronchial
10	chr8:90823600-90824600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr8:90823600-90824600	Weak transcription	Muscle Satellite Cultured Cells	--

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