Variant report

Variant	rs545009
Chromosome Location	chr11:66333598-66333599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66333517..66336306-chr11:66404884..66407774,3	K562	blood:
2	chr11:66333502..66336819-chr11:66382812..66384536,3	K562	blood:
3	chr11:66333502..66335839-chr11:66382927..66384488,2	K562	blood:
4	chr11:66333513..66337489-chr11:66382854..66385992,4	MCF-7	breast:
5	chr11:66311617..66317579-chr11:66325496..66333927,8	MCF-7	breast:
6	chr11:66327492..66329082-chr11:66331211..66334153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248643	Chromatin interaction
ENSG00000250105	Chromatin interaction
ENSG00000174165	Chromatin interaction
ENSG00000248746	Chromatin interaction
ENSG00000173933	Chromatin interaction
ENSG00000239306	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10736656	0.85[ASN][1000 genomes]
rs10791882	0.94[ASN][1000 genomes]
rs1127894	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1671062	0.85[ASN][1000 genomes]
rs1671063	0.82[ASN][1000 genomes]
rs1671064	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671065	0.85[ASN][1000 genomes]
rs1700189	0.82[ASN][1000 genomes]
rs1791684	0.83[ASN][1000 genomes]
rs1791686	0.86[ASN][1000 genomes]
rs1815739	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000939	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3018318	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486584	0.93[ASN][1000 genomes]
rs503250	0.81[ASN][1000 genomes]
rs509556	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531490	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs540874	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556759	0.81[ASN][1000 genomes]
rs560556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618838	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs630021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs662094	0.83[AFR][1000 genomes]
rs677488	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs678397	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8432	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs545009	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs545009	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs545009	ACTN3	cis	Muscle Skeletal	GTEx
rs545009	CCS	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66326600-66334800	Weak transcription	Colon Smooth Muscle	Colon
3	chr11:66326800-66334800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:66326800-66334800	Weak transcription	Pancreas	Pancrea
5	chr11:66326800-66335000	Weak transcription	Psoas Muscle	Psoas
6	chr11:66326800-66335000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr11:66326800-66335200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:66326800-66335200	Weak transcription	Esophagus	oesophagus
9	chr11:66326800-66335200	Weak transcription	Left Ventricle	heart
10	chr11:66326800-66335200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:66327000-66335200	Weak transcription	Fetal Heart	heart
12	chr11:66327200-66335000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:66327400-66334600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr11:66327400-66335200	Weak transcription	Right Atrium	heart
15	chr11:66328000-66334000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:66328000-66334400	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr11:66328000-66335000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:66328200-66333600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr11:66328400-66334800	Strong transcription	Fetal Stomach	stomach
20	chr11:66329000-66334200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:66329000-66334600	Strong transcription	Brain Angular Gyrus	brain
22	chr11:66329000-66335000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:66329400-66333800	Strong transcription	Adipose Nuclei	Adipose
24	chr11:66329400-66333800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:66329400-66334200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:66329400-66334400	Strong transcription	Brain Hippocampus Middle	brain
27	chr11:66329400-66334800	Strong transcription	Brain Germinal Matrix	brain
28	chr11:66329400-66336600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:66329600-66333800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:66329600-66333800	Strong transcription	Brain Substantia Nigra	brain
31	chr11:66329800-66333800	Strong transcription	Fetal Brain Female	brain
32	chr11:66329800-66334600	Strong transcription	Brain Anterior Caudate	brain
33	chr11:66329800-66334600	Strong transcription	Brain Cingulate Gyrus	brain
34	chr11:66330400-66334400	Strong transcription	Ovary	ovary
35	chr11:66330400-66334800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr11:66330400-66335600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr11:66330400-66337800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:66330600-66336800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:66330800-66334800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:66330800-66335000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr11:66330800-66336000	Weak transcription	Fetal Lung	lung
42	chr11:66331000-66335600	Weak transcription	Aorta	Aorta
43	chr11:66331200-66333800	Strong transcription	Right Ventricle	heart
44	chr11:66331200-66334600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr11:66331200-66336600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:66331400-66333600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr11:66331400-66333600	Strong transcription	Liver	Liver
48	chr11:66331400-66333600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr11:66331400-66335200	Weak transcription	Colonic Mucosa	Colon
50	chr11:66331400-66337800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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