Variant report

Variant	rs2069522
Chromosome Location	chr15:75039233-75039234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr15:75039071-75039258	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74933643..74936641-chr15:75037979..75039941,2	K562	blood:
2	chr15:75037842..75040616-chr15:75043779..75046442,3	K562	blood:

Variant related genes	Relation type
CYP1A2	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11553762	0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs11631294	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631682	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11631689	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11631817	0.83[ASN][1000 genomes]
rs11632547	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632706	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632814	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632822	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11633539	0.82[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11633861	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636256	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637637	0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs16970078	0.82[ASW][hapmap]
rs16970170	0.82[ASW][hapmap]
rs16972511	0.82[ASW][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16972853	0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs17861124	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17861125	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17861130	0.93[ASN][1000 genomes]
rs17861138	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17861139	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17861141	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17861142	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17861145	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069519	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069521	1.00[CHB][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2069524	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069525	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069526	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35197434	0.93[ASN][1000 genomes]
rs35331038	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35408600	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4646425	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646427	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56066141	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56748048	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59902765	0.83[ASN][1000 genomes]
rs74025837	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74025839	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs74025842	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74025843	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74025847	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2069522	SCAMP5	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75023800-75041600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:75038800-75039400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr15:75039000-75039400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:75039200-75042400	Weak transcription	HepG2	liver

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