Variant report

Variant	rs10952913
Chromosome Location	chr7:87752528-87752529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10227241	0.85[CEU][hapmap]
rs10234048	0.89[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs10234412	0.92[CEU][hapmap]
rs10952910	0.85[CEU][hapmap]
rs10952914	0.85[CEU][hapmap]
rs11768853	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12535312	0.91[EUR][1000 genomes]
rs12535365	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12537586	0.91[EUR][1000 genomes]
rs12540117	0.82[EUR][1000 genomes]
rs13245213	0.80[CEU][hapmap]
rs17150161	0.94[YRI][hapmap]
rs2008834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2022555	0.90[YRI][hapmap]
rs2024018	0.90[YRI][hapmap]
rs2097918	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes]
rs2158766	0.90[YRI][hapmap]
rs2237541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282955	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs2282956	0.87[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs2282957	0.89[CEU][hapmap]
rs2299198	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2299199	0.96[CEU][hapmap];0.87[GIH][hapmap];0.82[EUR][1000 genomes]
rs2299200	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2301998	0.82[CEU][hapmap]
rs2373487	0.89[YRI][hapmap]
rs3753103	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4442059	0.92[CEU][hapmap]
rs4727151	0.88[CEU][hapmap]
rs4727152	0.85[CEU][hapmap]
rs4728731	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs6951172	0.89[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs6955194	0.89[CEU][hapmap]
rs6955696	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6957754	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958024	0.92[CEU][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap]
rs6968026	0.89[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs726328	0.85[CEU][hapmap]
rs7777040	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs7792853	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7793308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7799148	0.92[CEU][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs9632709	0.89[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs9641023	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023352	chr7:87418818-88192925	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539005	chr7:87418818-88192925	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv525073	chr7:87535096-87812968	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10952913	STEAP4	cis	cerebellum	SCAN
rs10952913	ADAM22	cis	Muscle Skeletal	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87741200-87782600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:87743400-87761800	Weak transcription	GM12878-XiMat	blood
3	chr7:87745000-87756600	Weak transcription	Fetal Intestine Small	intestine

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