Variant report

Variant	rs481354
Chromosome Location	chr1:84409393-84409394
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1811643	0.87[EUR][1000 genomes]
rs2182199	0.95[EUR][1000 genomes]
rs2892811	0.87[EUR][1000 genomes]
rs471151	0.89[EUR][1000 genomes]
rs484505	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs512737	0.82[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs522892	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs523531	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs532246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562971	0.87[EUR][1000 genomes]
rs566830	0.90[EUR][1000 genomes]
rs575577	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs592905	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs593763	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs593869	0.94[EUR][1000 genomes]
rs597594	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs602568	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs603447	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs615352	0.91[EUR][1000 genomes]
rs618232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs625107	0.90[EUR][1000 genomes]
rs626376	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs629277	0.83[EUR][1000 genomes]
rs649226	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6576955	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs659227	0.91[EUR][1000 genomes]
rs659743	0.91[EUR][1000 genomes]
rs664508	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666984	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs667304	0.89[EUR][1000 genomes]
rs669110	0.91[EUR][1000 genomes]
rs671209	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs671561	0.87[EUR][1000 genomes]
rs678794	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs680627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs680905	1.00[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs683074	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs684114	0.95[EUR][1000 genomes]
rs684651	0.90[EUR][1000 genomes]
rs726607	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7554866	0.83[ASN][1000 genomes]
rs810915	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs910184	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871551	chr1:84354464-84453223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs481354	LPHN2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84368400-84416600	Weak transcription	NHLF	lung
2	chr1:84368400-84428400	Weak transcription	Pancreas	Pancrea
3	chr1:84382600-84409800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:84387000-84410000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:84392200-84422400	Weak transcription	Fetal Stomach	stomach
6	chr1:84392400-84420400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:84399200-84429800	Weak transcription	HSMMtube	muscle
8	chr1:84403600-84426200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:84403600-84427400	Weak transcription	Fetal Brain Female	brain
10	chr1:84407400-84416400	Weak transcription	Brain Substantia Nigra	brain
11	chr1:84407800-84416400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:84408200-84416200	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:84408600-84409400	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr1:84408600-84409400	Strong transcription	HSMM	muscle
15	chr1:84408600-84409600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:84408800-84410400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links