Variant report

Variant	rs17045048
Chromosome Location	chr2:53871238-53871239
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10490465	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897282	0.89[ASW][hapmap];0.84[CEU][hapmap]
rs11900355	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11901698	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs13428687	0.93[ASN][1000 genomes]
rs13428898	0.96[ASN][1000 genomes]
rs17045037	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045065	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17045081	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17045084	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17045199	0.82[CHD][hapmap]
rs17520505	0.82[YRI][hapmap]
rs17521008	0.89[ASW][hapmap]
rs2302797	0.89[ASW][hapmap];0.84[CEU][hapmap]
rs2542571	0.86[CHD][hapmap]
rs2542581	0.89[ASW][hapmap];0.88[CEU][hapmap];0.82[TSI][hapmap]
rs2543629	0.81[ASW][hapmap];0.83[CEU][hapmap]
rs2692514	0.86[CHD][hapmap]
rs2692516	0.89[CHD][hapmap]
rs2692534	0.86[CHD][hapmap]
rs34408637	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3731970	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3770407	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3770408	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3770409	0.90[ASN][1000 genomes]
rs3770411	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs3930	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4525731	0.89[AMR][1000 genomes]
rs55861447	0.94[ASN][1000 genomes]
rs56081218	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56311225	0.94[ASN][1000 genomes]
rs56383522	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58125503	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58515086	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60282090	0.92[ASN][1000 genomes]
rs61671599	0.91[ASN][1000 genomes]
rs62139773	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62139774	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62139775	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62139785	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62139788	0.92[ASN][1000 genomes]
rs62139836	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs719127	0.84[CEU][hapmap]
rs72901209	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73934971	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7583622	0.88[CHD][hapmap]
rs7600981	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv874146	chr2:53772561-53872803	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv874147	chr2:53772561-53886799	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2762637	chr2:53783253-53871596	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17045048	PSME4	cis	cerebellum	SCAN
rs17045048	TSPYL6	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53869200-53872600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:53869200-53873200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:53869400-53873200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:53869400-53873200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:53869400-53873400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:53869400-53873600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:53869600-53873400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:53869600-53873800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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