Variant report

Variant	rs948373
Chromosome Location	chr18:30428049-30428050
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10853423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12954449	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16963902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1893246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941254	1.00[JPT][hapmap]
rs1941281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1941282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1941283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1941286	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941287	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155785	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6506993	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6650651	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6650652	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6650653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs714776	1.00[CEU][hapmap]
rs7228308	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097557	1.00[JPT][hapmap]
rs8098125	1.00[JPT][hapmap]
rs948368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952405	1.00[JPT][hapmap]
rs9962968	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9966484	1.00[JPT][hapmap]
rs9989606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758474	chr18:30383327-30574737	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2758720	chr18:30383327-30574737	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv32785	chr18:30413359-30471471	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs948373	SCGB1D2	trans	brain	seeQTL
rs948373	SCGB2A2	trans	brain	seeQTL
rs948373	PIP4K2B	trans	brain	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:30426800-30428200	Enhancers	Fetal Brain Male	brain
2	chr18:30427000-30428400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr18:30427000-30428600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr18:30427000-30429200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr18:30427200-30428200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr18:30427200-30428400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr18:30427400-30428200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:30427600-30428200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr18:30427600-30428400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr18:30427800-30428400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr18:30427800-30432000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links