Variant report

Variant	rs9806326
Chromosome Location	chr15:77605533-77605534
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015813	0.82[ASN][1000 genomes]
rs10519158	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11854466	0.93[ASN][1000 genomes]
rs11856084	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs11856513	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11857330	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12148274	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12324016	0.82[ASN][1000 genomes]
rs12324211	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12324366	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12324795	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12900110	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902106	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902434	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902446	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs12912084	0.80[ASN][1000 genomes]
rs12912963	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13380152	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1374201	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1446313	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1493699	0.82[ASN][1000 genomes]
rs16968730	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16968799	0.82[ASN][1000 genomes]
rs17385296	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17468413	0.84[ASN][1000 genomes]
rs17471480	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs17471697	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs1867780	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs2044453	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs2137977	0.93[ASN][1000 genomes]
rs2172587	0.82[ASN][1000 genomes]
rs2292594	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2307141	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2864840	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs34572155	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35651077	0.82[ASN][1000 genomes]
rs3784788	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs4592615	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886514	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886852	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4886857	0.93[ASN][1000 genomes]
rs4886863	0.80[ASN][1000 genomes]
rs56070388	0.86[ASN][1000 genomes]
rs58792939	0.86[ASN][1000 genomes]
rs60079927	0.93[ASN][1000 genomes]
rs60761381	0.82[ASN][1000 genomes]
rs62010566	0.82[ASN][1000 genomes]
rs7163620	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182221	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs74025104	0.86[ASN][1000 genomes]
rs74025105	0.93[ASN][1000 genomes]
rs74027549	0.81[ASN][1000 genomes]
rs7496431	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs883627	0.84[CEU][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs907398	0.93[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1044270	chr15:77534919-77611256	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv542445	chr15:77534919-77611256	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1040430	chr15:77584375-77676957	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv984094	chr15:77603568-77608639	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9806326	PSTPIP1	cis	multi-tissue	Pritchard
rs9806326	HMG20A	cis	parietal	SCAN
rs9806326	CYP1A2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77577200-77619400	Weak transcription	HSMM	muscle
2	chr15:77598800-77609800	Weak transcription	Brain Angular Gyrus	brain
3	chr15:77603000-77605600	Enhancers	HepG2	liver
4	chr15:77603400-77633400	Weak transcription	Primary B cells from cord blood	blood
5	chr15:77603600-77606000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:77603800-77606400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:77604000-77605600	Enhancers	HMEC	breast
8	chr15:77604000-77605800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:77604000-77605800	Enhancers	NHDF-Ad	bronchial
10	chr15:77604000-77606000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:77604800-77605600	Enhancers	Fetal Heart	heart
12	chr15:77605000-77608600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:77605000-77612400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:77605200-77609000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:77605200-77609000	Weak transcription	NHLF	lung
16	chr15:77605200-77612000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:77605200-77612200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:77605200-77612400	Weak transcription	Left Ventricle	heart
19	chr15:77605200-77618400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:77605200-77619400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:77605400-77607000	Weak transcription	Adipose Nuclei	Adipose
22	chr15:77605400-77612400	Weak transcription	Osteobl	bone

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