Variant report

Variant	rs315525
Chromosome Location	chr1:84813966-84813967
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1067072	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1246546	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1246549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1246550	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs160612	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1690702	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs1699157	0.92[ASN][1000 genomes]
rs170278	1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs17131592	0.94[GIH][hapmap]
rs17131617	0.94[GIH][hapmap]
rs172735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17536473	1.00[CEU][hapmap]
rs178367	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs178368	0.99[ASN][1000 genomes]
rs186405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2055115	1.00[CEU][hapmap]
rs315520	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs315521	0.99[ASN][1000 genomes]
rs315522	0.99[ASN][1000 genomes]
rs315523	0.99[ASN][1000 genomes]
rs315524	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs315527	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs315528	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]
rs315530	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs315531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs315532	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315533	0.93[ASN][1000 genomes]
rs315535	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315536	0.99[ASN][1000 genomes]
rs315538	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315539	0.93[ASN][1000 genomes]
rs315540	0.91[ASN][1000 genomes]
rs315546	0.99[ASN][1000 genomes]
rs315547	0.92[ASN][1000 genomes]
rs315548	0.99[ASN][1000 genomes]
rs315549	0.99[ASN][1000 genomes]
rs315552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs315553	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs315554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs315555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316644	0.81[CHD][hapmap];0.82[YRI][hapmap]
rs316660	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs316661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs316662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316663	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs316664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316665	1.00[ASN][1000 genomes]
rs511087	0.99[ASN][1000 genomes]
rs592464	1.00[ASN][1000 genomes]
rs786653	0.92[EUR][1000 genomes];0.92[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
rs315525	HIVEP2	trans	cerebellum	SCAN

Chromatin state (count:32 , 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	chr1:84810200-84819800	Weak transcription	HSMM	muscle
5	chr1:84810600-84814800	Weak transcription	Gastric	stomach
6	chr1:84810600-84815400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:84812200-84814200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:84812400-84814000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr1:84812400-84814200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:84812600-84814000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:84812600-84814000	Enhancers	Psoas Muscle	Psoas
12	chr1:84812800-84814000	Enhancers	NHLF	lung
13	chr1:84812800-84814200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:84813000-84814000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:84813000-84814400	Enhancers	NH-A	brain
16	chr1:84813200-84814000	Flanking Active TSS	Osteobl	bone
17	chr1:84813200-84814200	Enhancers	NHDF-Ad	bronchial
18	chr1:84813200-84814400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:84813200-84814600	Enhancers	HMEC	breast
20	chr1:84813200-84815200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:84813200-84815200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:84813600-84814000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:84813600-84814000	Enhancers	Stomach Smooth Muscle	stomach
24	chr1:84813600-84814200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:84813600-84815200	Weak transcription	Brain Anterior Caudate	brain
26	chr1:84813600-84816600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:84813800-84814200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:84813800-84814200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:84813800-84814200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:84813800-84814600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:84813800-84815000	Weak transcription	Fetal Intestine Small	intestine
32	chr1:84813800-84818000	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links