Variant report

Variant	rs34468460
Chromosome Location	chr1:223482641-223482642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223482285..223484073-chr1:223489102..223491218,2	K562	blood:
2	chr1:223482509..223485104-chr1:223493881..223496147,2	K562	blood:
3	chr1:223482285..223485128-chr1:223488818..223491218,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1341289	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1341291	0.82[JPT][hapmap];0.82[LWK][hapmap];0.89[YRI][hapmap]
rs1518040	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1539047	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17163762	0.89[YRI][hapmap]
rs17163773	0.82[LWK][hapmap];0.89[YRI][hapmap]
rs17163774	0.82[LWK][hapmap];0.89[YRI][hapmap]
rs17163787	0.84[AFR][1000 genomes]
rs17163789	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17163816	0.82[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17163818	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17163831	0.89[LWK][hapmap]
rs17487717	0.95[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1829308	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1829309	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1850562	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856933	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1935037	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1949441	0.91[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs2096082	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2138970	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176504	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176505	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]
rs2176506	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2203763	0.82[JPT][hapmap];0.87[LWK][hapmap];0.89[YRI][hapmap]
rs2795063	0.82[JPT][hapmap]
rs34238669	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34827745	0.84[AFR][1000 genomes]
rs4661238	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661239	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838234	0.81[AFR][1000 genomes]
rs61838235	0.81[AFR][1000 genomes]
rs61838236	0.81[AFR][1000 genomes]
rs61838237	0.81[AFR][1000 genomes]
rs61838241	0.80[AFR][1000 genomes]
rs66531524	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66768536	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66867621	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67707169	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7536652	0.84[LWK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs7541162	0.80[AFR][1000 genomes]
rs825127	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs825131	0.82[AMR][1000 genomes];0.87[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
rs34468460	SUSD4	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223470000-223493200	Weak transcription	Esophagus	oesophagus
2	chr1:223473000-223484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:223480800-223482800	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr1:223482200-223486600	Weak transcription	Ovary	ovary
5	chr1:223482200-223488200	Weak transcription	Fetal Thymus	thymus
6	chr1:223482200-223488600	Weak transcription	Primary T cells from cord blood	blood
7	chr1:223482200-223488600	Weak transcription	Thymus	Thymus

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