Variant report

Variant	rs4912450
Chromosome Location	chr1:86385876-86385877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10493777	0.96[CEU][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs10873734	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10873736	0.90[EUR][1000 genomes]
rs11812027	0.88[EUR][1000 genomes]
rs12032751	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12034125	0.90[EUR][1000 genomes]
rs12043396	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12088838	0.96[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs12133355	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12136742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858556	0.96[CEU][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs2174051	0.90[EUR][1000 genomes]
rs313719	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];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912448	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];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs533090	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs537550	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs556848	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs591634	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs606678	0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs607336	0.84[ASN][1000 genomes]
rs607979	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs608460	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs61785115	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625872	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs633028	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs658934	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6667008	0.86[EUR][1000 genomes]
rs668874	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][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];0.85[GIH][hapmap];0.85[MKK][hapmap];0.88[EUR][1000 genomes]
rs7536689	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs997439	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
4	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
5	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
6	esv1810714	chr1:86339811-86392577	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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
8	nsv462395	chr1:86379514-86457334	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv546726	chr1:86379514-86457334	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv546727	chr1:86381650-86416725	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1808295	chr1:86385776-86392071	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
12	esv1842487	chr1:86385776-86392071	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
13	nsv522304	chr1:86385876-86402244	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv546728	chr1:86385876-86403759	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv546729	chr1:86385876-86404496	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv437701	chr1:86385876-86416343	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4912450	KIAA1210	trans	parietal	SCAN
rs4912450	SH3GLB1	cis	cerebellum	SCAN
rs4912450	LOC339524	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86366800-86386400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:86381400-86386000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:86384800-86387800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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