Variant report

Variant	rs712857
Chromosome Location	chr1:223434633-223434634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223423415..223426395-chr1:223432368..223434793,2	MCF-7	breast:
2	chr1:223434545..223436405-chr1:223440179..223441751,2	K562	blood:
3	chr1:223432400..223434848-chr1:223436145..223437894,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1400961	0.82[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1418150	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1418152	0.81[TSI][hapmap]
rs1640846	0.92[EUR][1000 genomes]
rs1640849	0.83[ASW][hapmap];0.85[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs17161988	0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17163765	0.83[ASW][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs17576822	0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs1773710	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1773713	0.92[EUR][1000 genomes]
rs35133329	0.89[AFR][1000 genomes]
rs3820596	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[LWK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61837627	0.92[EUR][1000 genomes]
rs61837629	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61837630	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61837633	0.80[EUR][1000 genomes]
rs61837635	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs712858	0.93[EUR][1000 genomes]
rs73122234	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74145795	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs851194	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs851196	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs851201	0.96[CEU][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs885279	0.88[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9442040	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	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
3	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs712857	SUSD4	cis	cerebellum	SCAN
rs712857	SUSD4	cis	parietal	SCAN
rs712857	WDR26	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223423800-223439600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:223424200-223438800	Weak transcription	Ovary	ovary
3	chr1:223427400-223442000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:223432200-223440200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:223432400-223442200	Weak transcription	Pancreas	Pancrea
6	chr1:223432600-223438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:223433200-223444600	Weak transcription	Esophagus	oesophagus
8	chr1:223433600-223440400	Weak transcription	Fetal Intestine Large	intestine
9	chr1:223434400-223437400	Weak transcription	Primary T cells from cord blood	blood

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