Variant report

Variant	rs8002779
Chromosome Location	chr13:92015977-92015978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:92013384..92016331-chr13:92208566..92210959,3	K562	blood:
2	chr13:92014568..92016594-chr13:92120306..92123284,2	K562	blood:
3	chr13:92015353..92017050-chr13:92205508..92207403,2	K562	blood:
4	chr13:92013762..92017162-chr13:92191310..92194678,3	K562	blood:
5	chr13:92012879..92016310-chr13:92160976..92164923,4	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1330062	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1330063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1428	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3759452	0.86[GIH][hapmap]
rs4142965	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4284505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773624	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4773625	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7319045	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7319759	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7320878	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7322734	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7324173	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7336610	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs769040	0.88[YRI][hapmap]
rs8001004	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs932910	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9515919	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9523304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9523307	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9523310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9523312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9523313	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9523326	0.82[GIH][hapmap]
rs976547	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv832679	chr13:91859467-92030220	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1943 gene(s)	inside rSNPs	diseases
7	esv1802171	chr13:91999737-92015977	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1940 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	20189936	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8002779	GPC5	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92001800-92027200	Weak transcription	Aorta	Aorta
2	chr13:92003600-92016600	Weak transcription	Gastric	stomach
3	chr13:92003600-92021200	Weak transcription	Right Ventricle	heart
4	chr13:92003600-92033200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr13:92004600-92021200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:92008800-92021000	Weak transcription	Osteobl	bone
7	chr13:92008800-92021400	Weak transcription	NHLF	lung
8	chr13:92009200-92016200	Enhancers	Liver	Liver
9	chr13:92009400-92020000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr13:92009400-92020800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:92009600-92021200	Weak transcription	HSMMtube	muscle
12	chr13:92009600-92022200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:92009800-92021200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr13:92009800-92021200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr13:92010000-92021000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr13:92010000-92021000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr13:92010200-92021200	Weak transcription	NH-A	brain
18	chr13:92010200-92021600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr13:92010400-92021400	Weak transcription	HMEC	breast
20	chr13:92010600-92021200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:92010800-92020800	Weak transcription	HSMM	muscle
22	chr13:92010800-92021000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:92010800-92021000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:92010800-92021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:92010800-92021200	Weak transcription	HUVEC	blood vessel
26	chr13:92010800-92026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr13:92011000-92017200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr13:92011000-92021000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr13:92011000-92021000	Weak transcription	Psoas Muscle	Psoas
30	chr13:92011000-92021200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr13:92011400-92020600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:92011800-92016400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr13:92011800-92020600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr13:92011800-92020600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr13:92013200-92021400	Weak transcription	K562	blood
36	chr13:92013400-92020000	Weak transcription	GM12878-XiMat	blood
37	chr13:92014600-92021800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:92014600-92022000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr13:92015000-92017000	Weak transcription	A549	lung
40	chr13:92015000-92021000	Weak transcription	NHEK	skin
41	chr13:92015200-92016200	Enhancers	HepG2	liver
42	chr13:92015600-92021600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:92015800-92021400	Weak transcription	Ovary	ovary

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