Variant report

Variant	rs315528
Chromosome Location	chr1:84810396-84810397
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1067072	0.92[ASN][1000 genomes]
rs1246546	1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs1246549	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1246550	0.90[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs160612	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1690702	0.89[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1699157	0.92[ASN][1000 genomes]
rs170278	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17131613	1.00[GIH][hapmap]
rs172735	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17536473	1.00[CEU][hapmap]
rs178367	0.94[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs178368	0.91[ASN][1000 genomes]
rs186405	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055115	1.00[CEU][hapmap]
rs315520	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs315521	0.91[ASN][1000 genomes]
rs315522	0.91[ASN][1000 genomes]
rs315523	0.91[ASN][1000 genomes]
rs315524	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs315525	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315526	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs315527	0.89[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs315530	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs315531	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315532	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs315533	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs315535	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs315536	0.91[ASN][1000 genomes]
rs315538	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs315539	0.99[ASN][1000 genomes]
rs315540	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs315542	0.82[AMR][1000 genomes]
rs315546	0.91[ASN][1000 genomes]
rs315547	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs315548	0.91[ASN][1000 genomes]
rs315549	0.91[ASN][1000 genomes]
rs315552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315553	0.94[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs315554	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs315555	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315556	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316660	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs316661	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs316662	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs316663	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs316664	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316665	0.92[ASN][1000 genomes]
rs511087	0.91[ASN][1000 genomes]
rs592464	0.92[ASN][1000 genomes]
rs786653	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs315528	HIVEP2	trans	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84795800-84827000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:84801400-84815000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:84802800-84815600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:84805800-84813800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:84809800-84810400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:84809800-84810400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:84809800-84810400	Enhancers	K562	blood
8	chr1:84809800-84810600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:84809800-84810600	Enhancers	Osteobl	bone
10	chr1:84809800-84811200	Enhancers	NHDF-Ad	bronchial
11	chr1:84809800-84811400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:84809800-84811400	Enhancers	NHLF	lung
13	chr1:84810000-84810600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:84810000-84810600	Enhancers	Gastric	stomach
15	chr1:84810000-84811400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:84810200-84810400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:84810200-84810400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:84810200-84810600	Flanking Active TSS	NH-A	brain
19	chr1:84810200-84811200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:84810200-84813200	Weak transcription	HMEC	breast
21	chr1:84810200-84813400	Weak transcription	Fetal Intestine Small	intestine
22	chr1:84810200-84813800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:84810200-84819800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links