Variant report

Variant	rs2176505
Chromosome Location	chr1:223487055-223487056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1341289	0.88[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1341291	0.82[JPT][hapmap];0.89[YRI][hapmap]
rs1518040	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1539047	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17163762	0.89[YRI][hapmap]
rs17163773	0.89[YRI][hapmap]
rs17163774	0.89[YRI][hapmap]
rs17163787	0.86[AFR][1000 genomes]
rs17163789	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17163816	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17163818	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17163831	0.84[LWK][hapmap]
rs17487717	1.00[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1829308	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1829309	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1850562	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856933	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1935037	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1949441	0.95[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2096082	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2138970	0.88[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176506	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2203763	0.82[JPT][hapmap];0.82[LWK][hapmap];0.89[YRI][hapmap]
rs2795063	0.82[JPT][hapmap]
rs34238669	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34468460	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34827745	0.81[AFR][1000 genomes]
rs4661238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838234	0.80[AFR][1000 genomes]
rs61838235	0.80[AFR][1000 genomes]
rs61838236	0.82[AFR][1000 genomes]
rs61838237	0.82[AFR][1000 genomes]
rs61838241	0.81[AFR][1000 genomes]
rs66531524	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66768536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66867621	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67707169	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7536652	0.84[LWK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs825127	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs825131	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs885279	0.82[YRI][hapmap]

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	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
3	nsv518979	chr1:223468336-223488310	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2176505	SUSD4	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223470000-223493200	Weak transcription	Esophagus	oesophagus
2	chr1:223482200-223488200	Weak transcription	Fetal Thymus	thymus
3	chr1:223482200-223488600	Weak transcription	Primary T cells from cord blood	blood
4	chr1:223482200-223488600	Weak transcription	Thymus	Thymus
5	chr1:223485800-223487400	Enhancers	Stomach Smooth Muscle	stomach
6	chr1:223486600-223487200	Enhancers	Ovary	ovary

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