Variant report

Variant	rs4799677
Chromosome Location	chr18:30490218-30490219
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10853423	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11081789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11660802	1.00[ASN][1000 genomes]
rs12457058	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954449	1.00[JPT][hapmap]
rs1539817	1.00[ASN][1000 genomes]
rs16963902	1.00[JPT][hapmap]
rs1893245	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893246	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1941254	1.00[JPT][hapmap]
rs1941261	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941262	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941265	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941267	1.00[ASN][1000 genomes]
rs1941270	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941271	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941281	1.00[JPT][hapmap]
rs1941282	1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1941283	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs2000653	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032183	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155785	1.00[ASN][1000 genomes]
rs2155786	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2226696	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411577	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799337	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799671	1.00[ASN][1000 genomes]
rs4799675	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799676	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506993	1.00[ASN][1000 genomes]
rs6506996	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650651	1.00[ASN][1000 genomes]
rs6650652	1.00[ASN][1000 genomes]
rs6650653	1.00[ASN][1000 genomes]
rs7228416	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7230824	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231153	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232256	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235150	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7241267	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955293	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955296	1.00[EUR][1000 genomes]
rs768140	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768141	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8090702	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091086	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097557	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8098125	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304114	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948368	1.00[JPT][hapmap]
rs948375	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950067	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952405	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962968	1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9966484	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989606	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv2250	chr18:30473758-30505927	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1060448	chr18:30481131-30540347	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1056985	chr18:30486272-30540347	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv1816769	chr18:30486596-30518855	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4799677	SCGB2A2	trans	brain	seeQTL
rs4799677	SCGB1D2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:30487000-30490400	Weak transcription	HMEC	breast
2	chr18:30487200-30490400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:30487800-30490800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr18:30487800-30490800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:30488400-30491200	Enhancers	Primary B cells from peripheral blood	blood
6	chr18:30488400-30492200	Enhancers	Primary B cells from cord blood	blood
7	chr18:30489400-30491800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:30489600-30491000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr18:30489800-30490600	Enhancers	NH-A	brain
10	chr18:30489800-30490800	Enhancers	HepG2	liver
11	chr18:30489800-30491000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:30490000-30490400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr18:30490200-30491000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr18:30490200-30491200	Enhancers	Fetal Muscle Leg	muscle
15	chr18:30490200-30492200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links