Variant report

Variant	rs4912448
Chromosome Location	chr1:86357528-86357529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10493777	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs10873734	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10873736	0.87[EUR][1000 genomes]
rs11812027	0.88[EUR][1000 genomes]
rs12032751	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs12034125	0.87[EUR][1000 genomes]
rs12043396	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12088838	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs12133355	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1858556	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs2174051	0.87[EUR][1000 genomes]
rs313719	0.95[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs313732	1.00[YRI][hapmap]
rs4146294	0.88[EUR][1000 genomes]
rs472286	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4912450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs491358	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs533090	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs556848	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs591634	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs606678	0.92[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs607979	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs608460	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs61785115	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs625872	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs633028	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs658934	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6667008	0.84[EUR][1000 genomes]
rs668874	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs6703317	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6703454	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs729102	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[EUR][1000 genomes]
rs7536689	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs997439	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1011293	chr1:86270649-86416972	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv871189	chr1:86315724-86402244	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv1810714	chr1:86339811-86392577	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv870724	chr1:86352810-86402244	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4912448	LOC339524	cis	cerebellum	SCAN
rs4912448	SH3GLB1	cis	cerebellum	SCAN
rs4912448	KIAA1210	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86342400-86370600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:86345600-86370600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:86347000-86366000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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