Variant report

Variant	rs12539945
Chromosome Location	chr7:16122473-16122474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:16121252..16122789-chr7:16129191..16131014,2	K562	blood:

Variant related genes	Relation type
ENSG00000230981	Chromatin interaction
ENSG00000273477	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10487911	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10950600	0.82[EUR][1000 genomes]
rs10950601	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10950604	0.81[EUR][1000 genomes]
rs11760631	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11760717	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11762563	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11766276	0.81[EUR][1000 genomes]
rs11773533	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12533693	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12537658	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12539174	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12667418	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12699766	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12699769	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13221870	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13231996	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13245773	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1405591	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1527203	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1527205	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17284967	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2240855	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28444529	0.84[EUR][1000 genomes]
rs34612021	0.81[EUR][1000 genomes]
rs66933521	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6959719	0.82[EUR][1000 genomes]
rs758702	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7777809	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7801576	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats 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 target site	56 gene(s)	inside rSNPs	diseases
2	nsv949309	chr7:15986709-16236162	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv949555	chr7:16078412-16279290	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16117200-16126400	Weak transcription	Aorta	Aorta
2	chr7:16118200-16129400	Weak transcription	Fetal Muscle Leg	muscle
3	chr7:16118400-16123000	Weak transcription	HUVEC	blood vessel
4	chr7:16120000-16123000	Weak transcription	HMEC	breast
5	chr7:16120000-16123400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:16121200-16123200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:16121800-16126400	Weak transcription	Gastric	stomach
8	chr7:16122200-16133000	Weak transcription	Psoas Muscle	Psoas
9	chr7:16122400-16135400	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links