Variant report

Variant	rs12044734
Chromosome Location	chr1:84853142-84853143
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12039378	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042948	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12568281	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275571	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs315512	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs477253	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507863	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508767	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548310	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580171	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585935	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585958	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636484	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649845	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666062	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696653	0.93[EUR][1000 genomes]
rs7554646	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	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
2	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12044734	LPAR3	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84845600-84857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:84845800-84854800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:84846400-84856000	Weak transcription	NHLF	lung
4	chr1:84851800-84853400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:84852000-84857200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:84852200-84853800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:84852400-84853400	Enhancers	HMEC	breast
8	chr1:84852400-84853600	Enhancers	NHEK	skin
9	chr1:84852600-84853600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:84852800-84853600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:84852800-84853600	Enhancers	HUVEC	blood vessel
12	chr1:84853000-84853200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:84853000-84853400	Enhancers	Placenta	Placenta
14	chr1:84853000-84853600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:84853000-84853600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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