Variant report

Variant	rs17163765
Chromosome Location	chr1:223448352-223448353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1400961	0.88[ASW][hapmap];0.85[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1418150	0.85[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1418152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418153	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1640846	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1640849	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17161988	0.85[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs17479856	1.00[CEU][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17517952	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17518077	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17538964	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17576822	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17577025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17577212	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1773710	0.85[EUR][1000 genomes]
rs1773713	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1829310	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28561511	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3820596	0.83[ASW][hapmap];0.85[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs61837627	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61837629	0.89[EUR][1000 genomes]
rs61837630	0.89[EUR][1000 genomes]
rs61837633	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61837634	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61837635	0.93[EUR][1000 genomes]
rs61837636	0.87[EUR][1000 genomes]
rs61837638	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61837640	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61838191	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61838192	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61838194	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61838197	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61838199	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs712857	0.83[ASW][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs712858	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73122234	0.93[EUR][1000 genomes]
rs7412060	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74145795	0.89[EUR][1000 genomes]
rs7518292	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs851202	0.86[JPT][hapmap]
rs851203	0.86[JPT][hapmap]
rs851206	0.86[JPT][hapmap]
rs885279	0.94[ASW][hapmap];0.84[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9442040	0.81[EUR][1000 genomes]
rs9442043	0.95[AMR][1000 genomes];0.98[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17163765	SUSD4	cis	parietal	SCAN
rs17163765	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223440800-223465600	Weak transcription	Ovary	ovary
2	chr1:223442600-223462200	Weak transcription	Primary T cells from cord blood	blood
3	chr1:223443800-223472600	Weak transcription	Gastric	stomach
4	chr1:223446200-223449600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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