Variant report

Variant	rs17268040
Chromosome Location	chr2:53742374-53742375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10165742	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10167973	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10174983	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10183446	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10183776	0.83[AMR][1000 genomes]
rs10191277	0.84[AMR][1000 genomes]
rs10204173	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10204330	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10204468	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10204470	0.82[ASN][1000 genomes]
rs10206558	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10496025	0.97[ASN][1000 genomes]
rs10496026	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11125505	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11887670	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472781	0.82[AMR][1000 genomes]
rs13394011	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13394197	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13394939	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13416219	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13420695	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13427989	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13429824	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1472238	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1565796	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17189463	0.87[ASN][1000 genomes]
rs17189470	0.96[ASN][1000 genomes]
rs17268033	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671411	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4672452	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4672453	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4672456	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4672461	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4672464	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545352	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6742054	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6743847	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72618655	0.87[ASN][1000 genomes]
rs72618656	0.96[ASN][1000 genomes]
rs7559727	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7560576	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7571640	0.84[AMR][1000 genomes]
rs7577504	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7586356	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7586411	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7586468	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7586738	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7596693	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7596877	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7597009	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7599710	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603561	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7604056	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7607091	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs961241	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002145	chr2:53387912-53832213	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv535718	chr2:53387912-53832213	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv997401	chr2:53515629-53863347	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv999571	chr2:53690538-53775723	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1012754	chr2:53690538-53785037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv457873	chr2:53701324-53785037	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv582009	chr2:53701324-53785037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv457886	chr2:53722595-53835083	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv582010	chr2:53722595-53835083	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17268040	CCDC85A	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53733400-53744800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:53737200-53743400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:53737400-53747200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:53737800-53743200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:53738000-53744200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:53740000-53744200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:53740000-53747400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:53740600-53742800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:53741200-53743000	Weak transcription	Fetal Heart	heart
10	chr2:53742200-53742400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:53742200-53743400	Enhancers	Hela-S3	cervix
12	chr2:53742200-53743600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:53742200-53743600	Enhancers	Left Ventricle	heart

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