Variant report

Variant	rs9442047
Chromosome Location	chr1:223330743-223330744
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223316003..223317893-chr1:223330550..223332878,2	K562	blood:
2	chr1:223314512..223320175-chr1:223328849..223336149,9	MCF-7	breast:
3	chr1:223318487..223320795-chr1:223328403..223334378,5	K562	blood:

Variant related genes	Relation type
ENSG00000187554	Chromatin interaction
ENSG00000236846	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1341986	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1341987	0.88[ASW][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs17661703	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1773750	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1773755	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1773756	0.98[ASN][1000 genomes]
rs1773757	0.98[ASN][1000 genomes]
rs1773758	0.99[ASN][1000 genomes]
rs2096141	0.82[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs2096142	0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs2247421	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2353475	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2353476	0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs2353477	0.86[ASN][1000 genomes]
rs2487835	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2883182	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34849527	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35442320	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35511158	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5744105	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5744113	0.94[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5744129	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61837568	0.96[ASN][1000 genomes]
rs61837569	0.96[ASN][1000 genomes]
rs61837573	0.96[ASN][1000 genomes]
rs61837574	0.96[ASN][1000 genomes]
rs61837575	0.96[ASN][1000 genomes]
rs61837577	0.95[ASN][1000 genomes]
rs67947164	0.81[ASN][1000 genomes]
rs723960	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743865	0.96[ASN][1000 genomes]
rs851166	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs851171	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs851178	0.83[MEX][hapmap]
rs9442048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975089	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9442047	TLR5	cis	cerebellum	SCAN
rs9442047	SUSD4	cis	parietal	SCAN
rs9442047	EPRS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223327200-223334600	Weak transcription	Fetal Thymus	thymus
2	chr1:223329000-223331000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:223329200-223338600	Weak transcription	Placenta	Placenta

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