Variant report

Variant	rs10809923
Chromosome Location	chr9:13267800-13267801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:13266586..13268806-chr9:13275605..13278055,2	MCF-7	breast:
2	chr9:13266536..13270627-chr9:13277145..13281714,5	K562	blood:
3	chr9:13267404..13273261-chr9:13274037..13279578,8	K562	blood:

Variant related genes	Relation type
ENSG00000234740	Chromatin interaction
ENSG00000107186	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10738329	0.89[GIH][hapmap]
rs10809926	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790299	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283251	0.81[CEU][hapmap]
rs13290727	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13297131	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13297480	0.84[GIH][hapmap]
rs1330134	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1412112	0.89[GIH][hapmap]
rs16930206	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1854665	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888150	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980994	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149988	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101279	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34423860	1.00[ASN][1000 genomes]
rs34504254	1.00[ASN][1000 genomes]
rs34714632	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34862901	1.00[ASN][1000 genomes]
rs4392997	1.00[ASN][1000 genomes]
rs7029241	0.89[GIH][hapmap]
rs7047995	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71507372	1.00[ASN][1000 genomes]
rs7866658	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS 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	10 gene(s)	inside rSNPs	diseases
2	nsv892583	chr9:13166139-13350478	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv892584	chr9:13214871-13350478	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv427838	chr9:13229753-13393890	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10809923	MPDZ	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13189000-13268600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:13226800-13278000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr9:13240000-13278000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:13248000-13267800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:13248000-13268600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:13255000-13277200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:13256600-13269800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:13256800-13277600	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:13264600-13267800	Enhancers	Colon Smooth Muscle	Colon
10	chr9:13264600-13268400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:13264600-13269200	Enhancers	Osteobl	bone
12	chr9:13264800-13269800	Enhancers	Rectal Smooth Muscle	rectum
13	chr9:13265000-13267800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:13265000-13268600	Enhancers	Fetal Heart	heart
15	chr9:13265200-13268400	Weak transcription	NHLF	lung
16	chr9:13265200-13268600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr9:13265600-13267800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:13265600-13268800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:13265600-13278200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:13265800-13268600	Weak transcription	Left Ventricle	heart
21	chr9:13265800-13269600	Weak transcription	Aorta	Aorta
22	chr9:13265800-13271800	Weak transcription	Right Ventricle	heart
23	chr9:13265800-13275000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:13265800-13275000	Weak transcription	Fetal Stomach	stomach
25	chr9:13266000-13267800	Enhancers	Psoas Muscle	Psoas
26	chr9:13266000-13269400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr9:13266000-13275000	Weak transcription	Brain Angular Gyrus	brain
28	chr9:13266200-13267800	Enhancers	Brain Anterior Caudate	brain
29	chr9:13266200-13267800	Flanking Active TSS	HUVEC	blood vessel
30	chr9:13266200-13268000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr9:13266200-13268000	Enhancers	Fetal Lung	lung
32	chr9:13266200-13269400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr9:13266200-13275000	Weak transcription	Right Atrium	heart
34	chr9:13266400-13268000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:13266400-13268600	Weak transcription	Ovary	ovary
36	chr9:13266800-13268400	Enhancers	A549	lung
37	chr9:13267000-13268800	Weak transcription	Brain Substantia Nigra	brain
38	chr9:13267000-13269400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr9:13267000-13269600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:13267000-13271200	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:13267000-13274800	Weak transcription	Adipose Nuclei	Adipose
42	chr9:13267000-13275000	Weak transcription	Brain Germinal Matrix	brain
43	chr9:13267000-13275000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:13267000-13275000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:13267200-13268000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:13267200-13268200	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr9:13267200-13269200	Enhancers	Hela-S3	cervix
48	chr9:13267200-13269800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr9:13267400-13267800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:13267400-13267800	Flanking Active TSS	NH-A	brain

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