Variant report

Variant	rs11869286
Chromosome Location	chr17:37813856-37813857
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1018246	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1053651	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10852934	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs11651497	0.91[ASN][1000 genomes]
rs11658786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150298	0.86[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150603	0.88[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12453682	0.87[GIH][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs12940986	0.88[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs14050	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs1476278	0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1495099	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1495100	0.95[ASN][1000 genomes]
rs1495101	0.95[ASN][1000 genomes]
rs1495102	0.95[ASN][1000 genomes]
rs1565920	0.94[ASN][1000 genomes]
rs1565922	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.95[ASN][1000 genomes]
rs1874228	0.88[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1877031	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247862	0.91[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs2271308	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2271309	0.87[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2313171	0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2517952	0.86[ASN][1000 genomes]
rs2517953	0.88[ASN][1000 genomes]
rs2517954	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2517955	0.88[ASW][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs2517956	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2517957	0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2517958	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2517959	0.87[ASN][1000 genomes]
rs2517960	0.86[ASN][1000 genomes]
rs2934951	0.95[ASN][1000 genomes]
rs2934952	0.95[ASN][1000 genomes]
rs2934953	0.81[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2934956	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941503	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs2941504	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs2941505	0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2941506	0.85[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs2952151	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs2952152	0.94[ASN][1000 genomes]
rs33953566	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35734596	0.86[ASN][1000 genomes]
rs3751903	0.91[ASN][1000 genomes]
rs3764351	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3764352	0.81[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs3764353	0.91[ASN][1000 genomes]
rs3794712	0.87[ASN][1000 genomes]
rs3817160	0.91[ASN][1000 genomes]
rs407307	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794817	0.91[ASN][1000 genomes]
rs4795388	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs4795389	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4795390	0.91[ASN][1000 genomes]
rs732083	0.95[ASN][1000 genomes]
rs732084	0.95[ASN][1000 genomes]
rs8077172	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8078228	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs879606	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs881844	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903501	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs903502	0.81[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907087	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs907088	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs907089	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs907090	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs907094	0.81[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9303274	0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs931992	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs9675194	0.86[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9915323	0.82[CEU][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9972882	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv516757	chr17:37781849-37834541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv908213	chr17:37807698-37839493	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
HDL cholesterol	20686565	GWAS catalog
HDL cholesterol	24097068	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11869286	PGAP3	cis	Skin Sun Exposed Lower leg	GTEx
rs11869286	PGAP3	cis	lung	GTEx
rs11869286	PGAP3	cis	Heart Left Ventricle	GTEx
rs11869286	SLFN14	cis	parietal	SCAN
rs11869286	PGAP3	cis	Nerve Tibial	GTEx
rs11869286	HNF1B	cis	cerebellum	SCAN
rs11869286	SPACA3	cis	parietal	SCAN
rs11869286	PGAP3	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37795000-37814000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr17:37795000-37823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:37795200-37814000	Weak transcription	Aorta	Aorta
4	chr17:37795200-37814600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:37795400-37818000	Weak transcription	Fetal Kidney	kidney
6	chr17:37799800-37819600	Weak transcription	Osteobl	bone
7	chr17:37800000-37814000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr17:37800000-37815200	Weak transcription	HUVEC	blood vessel
9	chr17:37800000-37818600	Weak transcription	Hela-S3	cervix
10	chr17:37800000-37820000	Weak transcription	NH-A	brain
11	chr17:37800200-37816800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:37800400-37814000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:37800600-37816200	Weak transcription	NHEK	skin
14	chr17:37801000-37814600	Weak transcription	Primary B cells from cord blood	blood
15	chr17:37801800-37817000	Weak transcription	A549	lung
16	chr17:37803400-37814200	Strong transcription	Thymus	Thymus
17	chr17:37803800-37821800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr17:37808400-37819200	Weak transcription	Small Intestine	intestine
19	chr17:37809200-37816200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:37809600-37814200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:37809800-37816400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:37809800-37819400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr17:37810000-37814000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr17:37810000-37815000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr17:37810000-37815600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr17:37810000-37817200	Weak transcription	HSMM	muscle
27	chr17:37810000-37819400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:37810000-37819600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr17:37810000-37820000	Weak transcription	HSMMtube	muscle
30	chr17:37810000-37820400	Strong transcription	Brain Germinal Matrix	brain
31	chr17:37810200-37814000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr17:37810200-37815400	Strong transcription	Fetal Stomach	stomach
33	chr17:37810200-37816200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr17:37810200-37816400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr17:37810200-37816400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:37810200-37816600	Strong transcription	Spleen	Spleen
37	chr17:37810200-37819800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr17:37810400-37814000	Weak transcription	Colon Smooth Muscle	Colon
39	chr17:37810400-37815000	Weak transcription	Pancreas	Pancrea
40	chr17:37810400-37817600	Weak transcription	Stomach Mucosa	stomach
41	chr17:37810400-37817800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr17:37810600-37814200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr17:37810600-37814200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr17:37810600-37814600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr17:37810600-37814600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr17:37810600-37814600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:37810600-37814600	Weak transcription	Liver	Liver
48	chr17:37810600-37815200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr17:37810600-37818600	Strong transcription	Fetal Intestine Small	intestine
50	chr17:37810600-37819200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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