Variant report

Variant	rs9991142
Chromosome Location	chr4:69932587-69932588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10025070	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249529	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs11931604	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11932983	0.93[ASN][1000 genomes]
rs11933432	0.84[ASN][1000 genomes]
rs11937195	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11945620	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11945705	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946976	0.93[ASN][1000 genomes]
rs12499192	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12506592	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12507173	0.93[ASN][1000 genomes]
rs12507556	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12508596	0.93[ASN][1000 genomes]
rs13136922	0.86[ASN][1000 genomes]
rs1841052	0.90[ASN][1000 genomes]
rs2125307	0.93[ASN][1000 genomes]
rs28365062	0.87[ASN][1000 genomes]
rs34545777	0.97[ASN][1000 genomes]
rs34561399	0.87[ASN][1000 genomes]
rs4259121	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343788	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4348159	0.80[ASN][1000 genomes]
rs4403109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4418041	0.93[ASN][1000 genomes]
rs4434329	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];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454001	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4554146	0.93[ASN][1000 genomes]
rs4694152	0.93[ASN][1000 genomes]
rs4694181	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs4694550	0.93[ASN][1000 genomes]
rs4694606	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55831171	0.90[ASN][1000 genomes]
rs55905314	0.87[ASN][1000 genomes]
rs56943005	0.93[ASN][1000 genomes]
rs57468707	0.93[ASN][1000 genomes]
rs58965335	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59314351	1.00[ASN][1000 genomes]
rs59732068	0.93[ASN][1000 genomes]
rs60276248	0.93[ASN][1000 genomes]
rs62296919	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62296941	0.87[ASN][1000 genomes]
rs62298861	0.83[ASN][1000 genomes]
rs62298872	0.90[ASN][1000 genomes]
rs62298898	0.82[ASN][1000 genomes]
rs66698711	0.87[ASN][1000 genomes]
rs6850028	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs72642938	0.93[ASN][1000 genomes]
rs72642947	0.93[ASN][1000 genomes]
rs72642961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7435335	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7680341	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv594582	chr4:69827340-69988378	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv879379	chr4:69878929-69987249	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv594583	chr4:69928642-69988378	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv427683	chr4:69929701-70414172	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv522091	chr4:69932587-69988378	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9991142	NPFFR2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69925000-69932600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:69927400-69934400	Weak transcription	Liver	Liver
3	chr4:69930400-69936600	Weak transcription	HepG2	liver
4	chr4:69930600-69932600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:69930600-69944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:69932400-69933000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:69932400-69933200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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