Variant report

Variant	rs4774760
Chromosome Location	chr15:55589212-55589213
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10851588	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11071174	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs11071176	0.85[ASN][1000 genomes]
rs11071180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071181	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11490399	0.86[ASN][1000 genomes]
rs11629613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11630409	0.87[ASN][1000 genomes]
rs11632757	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11634665	0.85[ASN][1000 genomes]
rs11635303	0.84[AMR][1000 genomes]
rs11635532	0.99[ASN][1000 genomes]
rs11636687	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638111	0.91[ASN][1000 genomes]
rs11638732	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11639418	0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs11639453	1.00[ASN][1000 genomes]
rs11855382	0.80[ASN][1000 genomes]
rs11857303	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050587	0.94[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12050662	0.86[ASN][1000 genomes]
rs12050663	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12050885	0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs12050905	0.90[ASN][1000 genomes]
rs2290341	0.94[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2290343	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290344	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2305424	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2414409	0.94[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs28540063	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28636865	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28657774	0.90[ASN][1000 genomes]
rs28668016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28680176	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs28706887	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28748576	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34848296	0.88[ASN][1000 genomes]
rs3743203	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4261468	0.85[GIH][hapmap]
rs4774764	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4774766	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55661134	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55933611	0.95[ASN][1000 genomes]
rs55957229	0.85[ASN][1000 genomes]
rs56159619	0.85[ASN][1000 genomes]
rs56257633	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58701687	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60338710	0.88[ASN][1000 genomes]
rs60375490	0.85[ASN][1000 genomes]
rs61387252	0.85[ASN][1000 genomes]
rs61573749	0.88[ASN][1000 genomes]
rs67230579	0.98[ASN][1000 genomes]
rs67603645	0.94[ASN][1000 genomes]
rs7162777	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174876	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7183157	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7183960	0.94[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs72742273	1.00[ASN][1000 genomes]
rs72742282	0.87[ASN][1000 genomes]
rs8024695	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs8034229	0.84[ASN][1000 genomes]
rs9920058	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9920522	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv1036924	chr15:55527874-55616480	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569522	chr15:55532211-55611126	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv904241	chr15:55534342-55611126	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv904242	chr15:55550755-55611126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv569524	chr15:55558624-55612511	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4774760	PIGB	cis	lymphoblastoid	seeQTL
rs4774760	PIGB	cis	multi-tissue	Pritchard
rs4774760	RAB27A	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55582600-55601400	Weak transcription	Lung	lung
2	chr15:55583000-55590600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr15:55583000-55596800	Weak transcription	Primary B cells from cord blood	blood
4	chr15:55583000-55597000	Weak transcription	Fetal Stomach	stomach
5	chr15:55583200-55597000	Weak transcription	Fetal Lung	lung
6	chr15:55583200-55597200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:55583200-55603000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:55583200-55603400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:55583200-55604400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:55583200-55610400	Weak transcription	Pancreas	Pancrea
11	chr15:55583400-55604400	Weak transcription	A549	lung
12	chr15:55584800-55597000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:55585200-55589800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr15:55585200-55589800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:55588800-55590000	Enhancers	K562	blood
16	chr15:55589200-55589800	Enhancers	Fetal Intestine Small	intestine
17	chr15:55589200-55590000	Enhancers	HepG2	liver

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