Variant report

Variant	rs12569293
Chromosome Location	chr1:86320956-86320957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86078662..86080625-chr1:86320837..86323478,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11161674	1.00[CEU][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11578980	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11588668	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11589719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11589722	1.00[CHB][hapmap]
rs11799965	0.92[CHB][hapmap]
rs11801550	1.00[CEU][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs11803202	0.92[CHB][hapmap]
rs11811165	0.92[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs12562000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12564528	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes]
rs12567327	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12755267	1.00[CHB][hapmap]
rs17128135	0.88[AFR][1000 genomes]
rs17128505	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs17128521	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes]
rs2062760	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3753785	1.00[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs41289761	0.88[AFR][1000 genomes]
rs41289763	0.94[AFR][1000 genomes]
rs57947545	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs60021908	0.94[AFR][1000 genomes]
rs61215520	0.94[AFR][1000 genomes]
rs6681351	1.00[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs6695359	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7520146	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7529764	0.94[AFR][1000 genomes]
rs7551256	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7556366	1.00[CHB][hapmap]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12569293	SAA3P	trans	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86305000-86332600	Weak transcription	Fetal Lung	lung
2	chr1:86305200-86326600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:86316600-86322200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:86316600-86326400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:86316600-86327400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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