Variant report

Variant	rs4646568
Chromosome Location	chr15:58344290-58344291
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	chr15:58339367..58342167-chr15:58342533..58344499,3	K562	blood:
2	chr15:58343646..58346573-chr15:58595833..58597683,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10851630	0.93[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs10851631	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs10851633	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071365	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071366	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630835	0.87[ASN][1000 genomes]
rs11852540	0.98[ASN][1000 genomes]
rs11855259	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11857461	0.96[ASN][1000 genomes]
rs12148093	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12148907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs12901462	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs12903474	0.93[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs12903551	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12907038	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs12908953	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs12910113	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs12910752	0.94[ASN][1000 genomes]
rs12911071	0.94[ASN][1000 genomes]
rs12914590	0.98[ASN][1000 genomes]
rs12915693	0.98[ASN][1000 genomes]
rs12915901	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1372368	0.95[ASN][1000 genomes]
rs3204689	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs34871384	0.96[ASN][1000 genomes]
rs35246600	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35511675	0.87[ASN][1000 genomes]
rs3784260	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs3784262	0.93[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap]
rs3784263	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs4238326	0.96[CEU][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4369598	0.98[ASN][1000 genomes]
rs4646563	0.96[ASN][1000 genomes]
rs4646571	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646572	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646576	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646586	0.95[ASN][1000 genomes]
rs4646593	0.92[ASN][1000 genomes]
rs4646611	0.88[ASN][1000 genomes]
rs4646612	0.88[ASN][1000 genomes]
rs4646615	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4646616	0.93[CHB][hapmap]
rs4646636	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4646638	0.93[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4646640	0.93[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs7164408	0.81[ASN][1000 genomes]
rs7165247	0.93[CHB][hapmap];0.87[GIH][hapmap]
rs7495968	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs8031133	0.82[ASN][1000 genomes]
rs8032107	0.96[ASN][1000 genomes]
rs9325	0.93[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]

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	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv904261	chr15:58258424-58347260	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv569594	chr15:58336218-58347260	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv904262	chr15:58340072-58355798	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv904263	chr15:58340072-58437346	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv569595	chr15:58343146-58353335	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4646568	PYGO1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58342000-58344600	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr15:58342400-58344400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
3	chr15:58342400-58344600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
4	chr15:58342600-58344600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
5	chr15:58342800-58344600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:58343800-58344400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
7	chr15:58343800-58347200	Enhancers	Fetal Kidney	kidney
8	chr15:58344200-58344400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr15:58344200-58349000	Weak transcription	K562	blood

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