Variant report

Variant	rs12532009
Chromosome Location	chr7:39073752-39073753
allele	A/G
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	ELK4	chr7:39073527-39073770	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
POU6F2	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10248136	0.85[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10951588	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1116811	1.00[ASW][hapmap];1.00[CEU][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];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1116813	0.81[JPT][hapmap]
rs12667652	0.86[CHB][hapmap]
rs12670003	0.82[CHB][hapmap]
rs12701690	0.81[JPT][hapmap]
rs13234105	0.81[JPT][hapmap]
rs1358422	0.81[JPT][hapmap]
rs1525798	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs1527949	0.81[JPT][hapmap]
rs1527952	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs17171519	0.87[CHB][hapmap]
rs17171520	0.88[JPT][hapmap]
rs17171521	0.81[JPT][hapmap]
rs34099272	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35787066	0.81[JPT][hapmap]
rs59514011	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62442164	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62443626	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6462886	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs6944670	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs6945380	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs6952464	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs6974522	0.87[CHB][hapmap]
rs7779583	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7779853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7801660	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs940876	0.93[CHB][hapmap];0.80[YRI][hapmap]

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	nsv1024142	chr7:38978728-39300444	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv887967	chr7:39009307-39090698	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12532009	PSMA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39067400-39074200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:39072000-39075000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:39072200-39074000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:39072400-39083200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:39072800-39074000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:39073000-39073800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:39073400-39073800	Active TSS	Fetal Brain Female	brain
8	chr7:39073400-39074800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr7:39073600-39074000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:39073600-39074000	Enhancers	Brain Germinal Matrix	brain
11	chr7:39073600-39074400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:39073600-39074600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr7:39073600-39075800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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