Variant report

Variant	rs9806139
Chromosome Location	chr15:77905024-77905025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77904241..77907935-chr15:77912354..77915026,5	K562	blood:
2	chr15:77901988..77905265-chr15:77907024..77909154,3	MCF-7	breast:
3	chr15:77904297..77907501-chr15:77908507..77911725,4	K562	blood:
4	chr15:77900844..77903141-chr15:77904661..77906674,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1104815	0.94[CEU][hapmap]
rs11630235	0.94[CEU][hapmap]
rs11631894	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11633811	0.81[CEU][hapmap]
rs11636780	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11638351	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11638674	0.94[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16968998	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16968999	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28368579	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28477219	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28706124	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3144	0.84[ASW][hapmap];0.94[YRI][hapmap]
rs4286073	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886882	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4886884	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886885	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886886	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886887	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4886888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7171141	0.84[EUR][1000 genomes]
rs8039399	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs884527	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1036749	chr15:77884026-77912408	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv904419	chr15:77897197-77943935	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9806139	CYP1A2	cis	cerebellum	SCAN
rs9806139	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs9806139	CHRNA5	cis	parietal	SCAN
rs9806139	HMG20A	cis	parietal	SCAN
rs9806139	CHRNA5	cis	cerebellum	SCAN
rs9806139	STRA6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77898400-77906400	Weak transcription	Pancreas	Pancrea
2	chr15:77899200-77905800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr15:77899800-77906400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:77899800-77908000	Weak transcription	Ovary	ovary
5	chr15:77900200-77906200	Weak transcription	Fetal Intestine Small	intestine
6	chr15:77900400-77907400	Weak transcription	Left Ventricle	heart
7	chr15:77900800-77905400	Weak transcription	Fetal Stomach	stomach
8	chr15:77901000-77914200	Weak transcription	Right Atrium	heart
9	chr15:77901600-77912800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:77901800-77906200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:77902400-77905600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:77902600-77905200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr15:77902600-77905600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:77902600-77905800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr15:77903200-77905600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:77903600-77914000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:77903800-77905400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:77904200-77914400	Weak transcription	Brain Substantia Nigra	brain
19	chr15:77904200-77915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:77904600-77905200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:77904600-77905400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:77904600-77906600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:77904600-77909000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:77904600-77910000	Weak transcription	K562	blood
25	chr15:77904600-77914000	Weak transcription	Fetal Lung	lung
26	chr15:77904800-77905200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:77904800-77906400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:77904800-77906400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:77904800-77906400	Weak transcription	Spleen	Spleen
30	chr15:77904800-77907000	Weak transcription	Brain Angular Gyrus	brain
31	chr15:77904800-77907200	Weak transcription	Brain Anterior Caudate	brain
32	chr15:77904800-77907600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:77904800-77908000	Strong transcription	Brain Germinal Matrix	brain
34	chr15:77904800-77909600	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:77904800-77914200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:77905000-77905400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:77905000-77906200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:77905000-77906400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:77905000-77906400	Weak transcription	Colonic Mucosa	Colon
40	chr15:77905000-77906600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:77905000-77906600	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:77905000-77906800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:77905000-77909000	Strong transcription	Fetal Brain Female	brain

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