Variant report

Variant	rs4052539
Chromosome Location	chr11:18141442-18141443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:18141353-18141450	Fibrobl	skin:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:18141393-18141443	NH-A	brain:	n/a
2	chr11:18141393-18141443	K562	blood:	n/a
3	chr11:18141393-18141443	SKMC	muscle:	n/a
4	chr11:18141393-18141443	HNPCEpiC	eye:	n/a
5	chr11:18141393-18141443	AG10803	skin:	n/a
6	chr11:18141393-18141443	AoSMC	blood vessel:	n/a
7	chr11:18141393-18141443	CMK	blood:	n/a
8	chr11:18141393-18141443	ECC-1	luminal epithelium:	n/a
9	chr11:18141393-18141443	RPTEC	kidney:	n/a
10	chr11:18141393-18141443	AG09319	gingival:	n/a
11	chr11:18141393-18141443	HRPEpiC	eye:	n/a
12	chr11:18141393-18141443	NT2-D1	testis:	n/a
13	chr11:18141393-18141443	HMEC	breast:	n/a
14	chr11:18141393-18141443	MCF-7	breast:	n/a
15	chr11:18141393-18141443	PFSK-1	brain:	n/a
16	chr11:18141393-18141443	Jurkat	blood:	n/a
17	chr11:18141393-18141443	PANC-1	pancreas:	n/a
18	chr11:18141393-18141443	AG04450	lung:	fetal
19	chr11:18141393-18141443	A549	lung:	n/a
20	chr11:18141393-18141443	GM12892	blood:	n/a
21	chr11:18141393-18141443	HCT-116	colon:	n/a
22	chr11:18141393-18141443	GM12891	blood:	n/a
23	chr11:18141393-18141443	U87	brain:	n/a
24	chr11:18141393-18141443	SK-N-MC	brain:	n/a
25	chr11:18141393-18141443	GM19239	blood:	n/a
26	chr11:18141393-18141443	NB4	blood:	n/a
27	chr11:18141393-18141443	GM12878	blood:	n/a
28	chr11:18141393-18141443	Hela-S3	cervix:	n/a
29	chr11:18141393-18141443	Hepatocyte	liver:	n/a
30	chr11:18141393-18141443	HAEpiC	amniotic membrane:	n/a
31	chr11:18141393-18141443	HRCEpiC	kidney:	n/a
32	chr11:18141393-18141443	HCM	heart:	n/a
33	chr11:18141393-18141443	PrEC	prostate:	n/a
34	chr11:18141393-18141443	HL-60	blood:	n/a
35	chr11:18141393-18141443	SK-N-SH	brain:	n/a
36	chr11:18141393-18141443	HepG2	liver:	n/a
37	chr11:18141393-18141443	T-47D	breast:	n/a
38	chr11:18141393-18141443	HEEpiC	esophagus:	n/a
39	chr11:18141393-18141443	ovcar-3	ovarian:	n/a
40	chr11:18141393-18141443	HIPEpiC	eye:	n/a
41	chr11:18141393-18141443	NHDF-neo	bronchial:	n/a
42	chr11:18141393-18141443	HCPEpiC	choroid plexus:	n/a
43	chr11:18141393-18141443	NHBE	bronchial:	n/a
44	chr11:18141393-18141443	HCF	heart:	n/a
45	chr11:18141393-18141443	ProgFib	skin:	n/a
46	chr11:18141393-18141443	MCF10A-Er-Src	breast:	n/a
47	chr11:18141393-18141443	AG04449	skin:	fetal
48	chr11:18141393-18141443	SAEC	small airway:	n/a
49	chr11:18141393-18141443	HEK293	kidney:	embryo
50	chr11:18141393-18141443	AG09309	skin:	n/a

No data

Variant related genes	Relation type
MRGPRX3	TF binding region
SAA3P	TF binding region
SAA3P	CpG island
MRGPRX3	CpG island

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10500831	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs10832882	0.96[ASN][1000 genomes]
rs11024460	0.83[CEU][hapmap]
rs11024468	0.96[ASN][1000 genomes]
rs11024474	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11024476	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs11024478	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11024482	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs11024484	0.96[ASN][1000 genomes]
rs11024485	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs11024489	0.86[ASN][1000 genomes]
rs11024493	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024496	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12360537	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12363226	0.96[ASN][1000 genomes]
rs12364327	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs12792460	0.81[ASN][1000 genomes]
rs1399025	0.90[CHB][hapmap]
rs1824017	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1840595	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1975777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2085275	0.82[CHB][hapmap]
rs2168361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2468832	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2468841	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2468842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2956631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35447333	0.81[ASN][1000 genomes]
rs3741199	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs4274188	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4756930	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap]
rs5790015	0.96[ASN][1000 genomes]
rs61882530	0.96[ASN][1000 genomes]
rs6486406	0.80[CHD][hapmap]
rs7119063	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs7131255	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs7131454	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7933259	0.85[ASN][1000 genomes]
rs7934091	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7942794	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs7943725	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs871699	0.90[CHB][hapmap]
rs907922	0.90[CHB][hapmap]
rs907923	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs964834	0.90[CHB][hapmap];0.83[JPT][hapmap]

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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv982925	chr11:18132176-18153921	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv11709	chr11:18138662-18200717	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4052539	SAAL1	cis	lung	GTEx
rs4052539	MRGPRX3	cis	Esophagus Mucosa	GTEx
rs4052539	SAAL1	cis	cerebellum	SCAN
rs4052539	SAAL1	cis	parietal	SCAN
rs4052539	SAAL1	cis	lymphoblastoid	seeQTL
rs4052539	SAAL1	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18136600-18141600	Enhancers	HepG2	liver
2	chr11:18136800-18141600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr11:18137400-18141600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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