Variant report

Variant	rs7779853
Chromosome Location	chr7:39057741-39057742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39056885..39058530-chr7:39059051..39061943,3	K562	blood:
2	chr7:39044098..39047140-chr7:39057342..39060274,3	K562	blood:
3	chr7:39052158..39055296-chr7:39055387..39058245,4	K562	blood:
4	chr7:39056516..39058385-chr7:39059051..39061295,2	K562	blood:

Variant related genes	Relation type
ENSG00000106536	Chromatin interaction
ENSG00000233854	Chromatin interaction

Extended variants
information (count: 32 )
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];0.90[ASN][1000 genomes]
rs10951588	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1116813	0.81[JPT][hapmap]
rs12532009	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]
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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35787066	0.81[JPT][hapmap]
rs59514011	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62442164	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62443626	0.91[AMR][1000 genomes];0.97[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830967	chr7:38913837-39069253	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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
rs7779853	PSMA2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39054200-39062000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:39056200-39058000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr7:39056400-39058000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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