Variant report

Variant	rs5744174
Chromosome Location	chr1:223284528-223284529
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	chr1:223280817..223282903-chr1:223283334..223285071,2	MCF-7	breast:
2	chr1:223283377..223285356-chr1:223290316..223292378,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10443637	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10443638	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10443639	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10443640	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1100886	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1100887	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729658	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12748315	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1640840	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1773714	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1773718	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1773726	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1773727	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1773729	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861172	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430402	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430403	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2487831	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2487833	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28460738	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28499047	0.84[EUR][1000 genomes]
rs28522106	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28594689	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28691199	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28880136	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34253986	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35251562	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3795742	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795743	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4661281	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4661282	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61840078	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61840137	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61840138	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61840140	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61840141	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61840142	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs712866	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7547359	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs851134	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851135	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851136	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs851137	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851138	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851139	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs851178	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851179	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs851180	0.90[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851181	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851183	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851184	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851185	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs851186	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs851187	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851188	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs851189	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs851190	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs851192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851193	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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs864834	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs877327	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887947	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5744174	C1orf58	cis	parietal	SCAN
rs5744174	TLR5	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223276600-223287400	Weak transcription	Right Atrium	heart
2	chr1:223276600-223287600	Weak transcription	Right Ventricle	heart
3	chr1:223276800-223287400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:223276800-223302200	Weak transcription	Esophagus	oesophagus
5	chr1:223277000-223306800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:223280400-223287200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:223281400-223286200	Enhancers	Fetal Intestine Small	intestine
8	chr1:223281600-223285400	Weak transcription	Lung	lung
9	chr1:223281800-223284600	Enhancers	Stomach Mucosa	stomach
10	chr1:223282000-223285800	Enhancers	Fetal Intestine Large	intestine
11	chr1:223282400-223302800	Weak transcription	Thymus	Thymus
12	chr1:223283200-223286400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:223283200-223287200	Weak transcription	Left Ventricle	heart
14	chr1:223283400-223302600	Weak transcription	Gastric	stomach
15	chr1:223283600-223288800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:223284000-223286200	Strong transcription	Ovary	ovary
17	chr1:223284200-223284800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:223284400-223284800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:223284400-223287200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:223284400-223287400	Weak transcription	HUVEC	blood vessel
21	chr1:223284400-223296800	Weak transcription	Pancreas	Pancrea

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