Variant report

Variant	rs11654069
Chromosome Location	chr17:16365086-16365087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16364123..16366452-chr17:16369978..16372148,2	MCF-7	breast:
2	chr17:16341296..16343840-chr17:16364793..16366455,2	K562	blood:
3	chr17:16364278..16365887-chr17:16371896..16373963,2	MCF-7	breast:
4	chr17:16342050..16344822-chr17:16364183..16367713,3	MCF-7	breast:
5	chr17:16363662..16365633-chr17:16366066..16368741,2	MCF-7	breast:
6	chr17:16364690..16366322-chr17:16367456..16369669,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266651	Chromatin interaction
ENSG00000175061	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11078342	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11078343	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11078344	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078345	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867498	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869614	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11870279	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11871017	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11871929	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11871958	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11871963	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12936240	0.81[AMR][1000 genomes]
rs12938294	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12940078	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17552310	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17715447	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34166276	0.81[AMR][1000 genomes]
rs34192401	0.81[AMR][1000 genomes]
rs34419652	0.81[AMR][1000 genomes]
rs34572942	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34577506	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34779276	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34793697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34850018	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34982046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35034622	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35247166	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35269706	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35377488	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35474528	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35540454	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35774281	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36117589	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56097826	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7217211	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs941411	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][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	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS 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 miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS 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	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh 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	99 gene(s)	inside rSNPs	diseases
8	nsv1065254	chr17:16252880-16389930	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
9	nsv428668	chr17:16265210-16455285	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
10	nsv1063941	chr17:16357086-16424098	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11654069	C17orf45	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16344600-16372800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr17:16345800-16373200	Weak transcription	Psoas Muscle	Psoas
3	chr17:16347000-16366400	Weak transcription	NHDF-Ad	bronchial
4	chr17:16347800-16367000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr17:16349000-16366600	Weak transcription	Right Atrium	heart
6	chr17:16350000-16366600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr17:16350200-16366600	Weak transcription	Fetal Lung	lung
8	chr17:16352600-16365600	Weak transcription	Adipose Nuclei	Adipose
9	chr17:16352600-16367400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr17:16352600-16369800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:16352600-16380800	Weak transcription	Aorta	Aorta
12	chr17:16352800-16365600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr17:16352800-16366400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:16352800-16366800	Weak transcription	Brain Hippocampus Middle	brain
15	chr17:16352800-16371000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr17:16352800-16375600	Weak transcription	Primary B cells from cord blood	blood
17	chr17:16352800-16376400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr17:16353400-16366800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr17:16353400-16367800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr17:16353400-16372200	Weak transcription	Osteobl	bone
21	chr17:16353600-16365400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr17:16354000-16370800	Weak transcription	K562	blood
23	chr17:16354400-16368600	Weak transcription	Esophagus	oesophagus
24	chr17:16354600-16366200	Weak transcription	Brain Angular Gyrus	brain
25	chr17:16356800-16366200	Weak transcription	Fetal Brain Male	brain
26	chr17:16356800-16367000	Weak transcription	Ovary	ovary
27	chr17:16356800-16377600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr17:16357000-16365200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:16357000-16366000	Weak transcription	Brain Substantia Nigra	brain
30	chr17:16357000-16366400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr17:16357200-16366200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:16357400-16365600	Weak transcription	HSMM	muscle
33	chr17:16358200-16365600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr17:16358600-16365800	Strong transcription	Fetal Stomach	stomach
35	chr17:16359600-16365400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr17:16359600-16366600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr17:16359800-16366800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr17:16360000-16365400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:16360600-16365400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr17:16360600-16377200	Weak transcription	Thymus	Thymus
41	chr17:16361000-16366800	Weak transcription	A549	lung
42	chr17:16361000-16376400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr17:16361600-16366000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr17:16362400-16367800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr17:16362600-16368200	Weak transcription	Brain Anterior Caudate	brain
46	chr17:16362800-16366800	Genic enhancers	Fetal Intestine Large	intestine
47	chr17:16363000-16366600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:16363000-16366800	Strong transcription	Brain Germinal Matrix	brain
49	chr17:16363200-16365600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr17:16363200-16366600	Strong transcription	Fetal Brain Female	brain

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