Variant report

Variant	rs8069576
Chromosome Location	chr17:19570320-19570321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19569611..19572312-chr17:19574479..19577295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11204408	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11656199	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11656773	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11871420	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12150145	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12941194	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17684040	0.91[EUR][1000 genomes]
rs1812051	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2108970	0.80[AMR][1000 genomes]
rs2108971	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120274	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2159291	0.81[AMR][1000 genomes]
rs2165895	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2245639	0.91[EUR][1000 genomes]
rs2386141	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386142	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386143	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386145	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440162	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2453586	0.91[EUR][1000 genomes]
rs2453600	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2453601	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2453604	0.91[EUR][1000 genomes]
rs2453608	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28495827	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28537694	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760489	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4273101	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4925036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109259	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62065943	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62065946	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587200	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587201	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7210433	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7215	0.85[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405861	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7405862	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7502992	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8069478	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074500	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8074784	0.84[EUR][1000 genomes]
rs8079648	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8081130	1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.80[YRI][hapmap]
rs962800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889632	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9903027	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv907865	chr17:19558722-19575721	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8069576	PIGL	cis	parietal	SCAN
rs8069576	ALDH3A2	cis	cerebellum	SCAN
rs8069576	MAP2K3	cis	cerebellum	SCAN
rs8069576	ALDH3A2	cis	parietal	SCAN
rs8069576	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19554800-19574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
6	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
8	chr17:19558400-19571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:19559200-19571800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:19559200-19574200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:19559400-19575000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:19559400-19575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:19559600-19570800	Strong transcription	Brain Anterior Caudate	brain
15	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:19559800-19577200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:19561200-19570600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr17:19564000-19581000	Weak transcription	Thymus	Thymus
19	chr17:19564400-19571000	Strong transcription	A549	lung
20	chr17:19564600-19571200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:19564800-19574600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr17:19565200-19570600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr17:19565400-19575800	Strong transcription	Fetal Stomach	stomach
24	chr17:19566000-19571200	Weak transcription	Fetal Thymus	thymus
25	chr17:19567000-19575800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr17:19567400-19574400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr17:19567400-19574400	Weak transcription	Fetal Heart	heart
28	chr17:19567400-19574800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr17:19567600-19574400	Weak transcription	Primary B cells from cord blood	blood
30	chr17:19567600-19574400	Weak transcription	Stomach Mucosa	stomach
31	chr17:19567600-19578600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr17:19567600-19584800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:19567800-19572800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr17:19567800-19574600	Weak transcription	NHDF-Ad	bronchial
35	chr17:19567800-19575200	Weak transcription	HSMM	muscle
36	chr17:19567800-19578600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:19568400-19573200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr17:19568400-19574400	Weak transcription	Right Atrium	heart
39	chr17:19568400-19574600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr17:19568400-19574600	Weak transcription	Hela-S3	cervix
41	chr17:19568400-19574800	Weak transcription	Osteobl	bone
42	chr17:19568400-19581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr17:19568600-19574200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr17:19568600-19575200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
46	chr17:19568800-19572800	Weak transcription	Primary T cells from cord blood	blood
47	chr17:19569000-19582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr17:19569200-19574400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr17:19569200-19574400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr17:19569400-19572800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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