Variant report

Variant	rs62025971
Chromosome Location	chr15:45073300-45073301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:44954130..44956261-chr15:45073217..45077809,7	K562	blood:
2	chr15:45017018..45019763-chr15:45071670..45073544,3	K562	blood:
3	chr15:45005930..45007757-chr15:45071632..45073366,2	K562	blood:
4	chr15:45020758..45022821-chr15:45070879..45074256,3	K562	blood:

Variant related genes	Relation type
ENSG00000166710	Chromatin interaction
ENSG00000185880	Chromatin interaction
ENSG00000104133	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1295357	0.80[EUR][1000 genomes]
rs1299814	0.96[EUR][1000 genomes]
rs1720727	0.96[EUR][1000 genomes]
rs17229438	0.85[EUR][1000 genomes]
rs17518229	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518621	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17588988	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17590443	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2123148	0.87[EUR][1000 genomes]
rs2443977	0.98[EUR][1000 genomes]
rs28489322	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28490581	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28733998	0.87[EUR][1000 genomes]
rs28857509	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2924121	0.89[EUR][1000 genomes]
rs35462944	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59030658	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62024992	0.87[EUR][1000 genomes]
rs62024993	0.87[EUR][1000 genomes]
rs62024994	0.87[EUR][1000 genomes]
rs62025030	0.85[EUR][1000 genomes]
rs62025031	0.91[EUR][1000 genomes]
rs62025036	0.93[EUR][1000 genomes]
rs62025965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62025966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62025998	0.91[EUR][1000 genomes]
rs7167663	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7168673	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170996	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7175365	0.87[EUR][1000 genomes]
rs7175751	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181308	0.87[EUR][1000 genomes]
rs7181488	0.87[EUR][1000 genomes]
rs7182388	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7182597	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7183658	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023272	0.87[EUR][1000 genomes]
rs8023794	0.87[EUR][1000 genomes]
rs8031964	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8033099	0.96[EUR][1000 genomes]
rs8036450	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8037029	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8042821	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8043138	0.87[EUR][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	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv819242	chr15:45059351-45078608	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62025971	TRIM69	cis	Artery Tibial	GTEx
rs62025971	TRIM69	cis	Muscle Skeletal	GTEx
rs62025971	TRIM69	cis	Artery Aorta	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45047600-45076000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr15:45057200-45076000	Weak transcription	Brain Anterior Caudate	brain
3	chr15:45068600-45073600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:45072600-45073600	Enhancers	Hela-S3	cervix
5	chr15:45072600-45073800	Enhancers	Brain Hippocampus Middle	brain
6	chr15:45072600-45073800	Enhancers	Brain Substantia Nigra	brain
7	chr15:45072600-45075800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:45072800-45073600	Enhancers	HepG2	liver
9	chr15:45072800-45074200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:45072800-45074200	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:45073000-45073400	Flanking Active TSS	K562	blood
12	chr15:45073000-45073600	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links