Variant report

Variant	rs39515
Chromosome Location	chr8:90828989-90828990
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	chr8:90827148..90830083-chr8:90913330..90915459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1003843	0.81[CHB][hapmap]
rs10112852	0.82[CHB][hapmap]
rs11989430	0.81[ASN][1000 genomes]
rs13280951	0.86[ASN][1000 genomes]
rs218907	0.82[CHB][hapmap]
rs218908	0.82[CHB][hapmap]
rs218913	0.81[CHB][hapmap]
rs218929	0.81[CHB][hapmap]
rs2338882	0.86[ASN][1000 genomes]
rs28144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28405481	0.81[ASN][1000 genomes]
rs28461337	0.86[ASN][1000 genomes]
rs2975240	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs368812	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs369771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs370282	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs374957	0.83[JPT][hapmap]
rs376110	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs383592	0.85[CEU][hapmap]
rs386857	0.84[JPT][hapmap]
rs394108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39501	0.80[CEU][hapmap]
rs39502	0.82[CEU][hapmap]
rs39509	0.86[CEU][hapmap];0.80[AMR][1000 genomes]
rs39516	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs39519	0.83[JPT][hapmap];0.87[YRI][hapmap]
rs39767	0.92[EUR][1000 genomes]
rs39768	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs39769	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs39771	0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs400411	0.80[AMR][1000 genomes]
rs400571	0.84[JPT][hapmap]
rs402434	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40247	0.82[CEU][hapmap]
rs40381	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40382	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40453	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs40457	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40458	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40547	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40636	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40637	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40638	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40639	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs410577	0.84[JPT][hapmap]
rs411279	0.81[CEU][hapmap]
rs416324	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs421411	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs422559	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42345	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42346	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs43133	0.80[CEU][hapmap]
rs43135	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs43136	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs43226	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs43227	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs43228	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs43229	0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs435600	0.81[EUR][1000 genomes]
rs438485	0.84[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs441548	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs445172	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs445675	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447611	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs452694	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs453266	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs454561	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs51331	0.86[CEU][hapmap]
rs62530862	0.85[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs39515	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs39515	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx
rs39515	RIPK2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90783800-90829000	Weak transcription	Aorta	Aorta
2	chr8:90824000-90836600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:90825400-90829400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:90825600-90829000	Weak transcription	NH-A	brain
5	chr8:90825800-90829000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:90826800-90829200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:90827800-90829200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:90828000-90829000	Weak transcription	NHDF-Ad	bronchial
9	chr8:90828000-90845800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr8:90828600-90829400	Enhancers	Osteobl	bone
11	chr8:90828800-90829400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:90828800-90829400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr8:90828800-90830600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links