Variant report

Variant	rs9788079
Chromosome Location	chr12:9484047-9484048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:9215856..9217597-chr12:9482273..9484056,2	MCF-7	breast:
2	chr12:9483967..9484695-chr12:9530892..9531873,3	MCF-7	breast:
3	chr12:9483454..9485642-chr12:9487208..9489749,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11050283	0.82[ASN][1000 genomes]
rs11611357	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12579328	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12580174	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12581470	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs12582622	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12828464	0.91[ASN][1000 genomes]
rs2003610	0.82[ASN][1000 genomes]
rs2003859	0.82[ASN][1000 genomes]
rs34181517	0.87[ASN][1000 genomes]
rs34285771	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34297500	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36066539	0.86[ASN][1000 genomes]
rs4141479	0.82[ASN][1000 genomes]
rs4636721	0.82[ASN][1000 genomes]
rs4883241	0.82[JPT][hapmap]
rs7294479	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs741623	0.81[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7959473	0.91[ASN][1000 genomes]
rs7971371	0.90[ASN][1000 genomes]
rs7972572	0.82[ASN][1000 genomes]
rs9788080	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788229	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788250	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv898742	chr12:9473157-9518222	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv898743	chr12:9473157-9522350	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv975403	chr12:9481646-9541991	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9788079	DDX12P	cis	Muscle Skeletal	GTEx
rs9788079	VWF	cis	cerebellum	SCAN
rs9788079	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs9788079	SLC2A14	cis	cerebellum	SCAN
rs9788079	DDX12P	cis	Artery Tibial	GTEx
rs9788079	RP11-22B23.1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9437200-9485200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:9457400-9485800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:9464600-9487600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:9464800-9490000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:9465000-9486400	Weak transcription	A549	lung
6	chr12:9465400-9485200	Weak transcription	Fetal Intestine Small	intestine
7	chr12:9465600-9488000	Weak transcription	Dnd41	blood
8	chr12:9466400-9485200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:9466400-9487200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:9466400-9487600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:9472800-9487600	Weak transcription	Thymus	Thymus
12	chr12:9479000-9486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:9479200-9486600	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:9480000-9485600	Weak transcription	HepG2	liver
15	chr12:9483800-9484200	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:9483800-9484200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:9483800-9484200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:9483800-9484200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:9483800-9484200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:9483800-9484200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:9483800-9484200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr12:9483800-9484800	Enhancers	Fetal Muscle Trunk	muscle
23	chr12:9483800-9485400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:9484000-9484200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr12:9484000-9484200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr12:9484000-9484200	Enhancers	Primary T cells from cord blood	blood
27	chr12:9484000-9484200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr12:9484000-9484200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:9484000-9484200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:9484000-9484200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:9484000-9484200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:9484000-9484200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:9484000-9484200	Enhancers	Brain Cingulate Gyrus	brain
34	chr12:9484000-9484200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr12:9484000-9484200	Enhancers	Duodenum Mucosa	Duodenum
36	chr12:9484000-9484200	Enhancers	Right Atrium	heart
37	chr12:9484000-9484200	Enhancers	Right Ventricle	heart
38	chr12:9484000-9484200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr12:9484000-9484200	Enhancers	K562	blood
40	chr12:9484000-9484400	Enhancers	Fetal Thymus	thymus
41	chr12:9484000-9484800	Flanking Active TSS	GM12878-XiMat	blood
42	chr12:9484000-9485000	Strong transcription	Fetal Lung	lung
43	chr12:9484000-9489000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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