Variant report

Variant	rs1934953
Chromosome Location	chr10:96797470-96797471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10786182	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10882514	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10882516	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10882523	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11188139	0.94[AFR][1000 genomes]
rs11188170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11572120	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11593160	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1341163	0.81[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1579029	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856908	0.84[MEX][hapmap]
rs1891071	0.81[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1891072	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926705	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1934973	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1934979	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1934984	0.85[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1934985	0.81[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2253635	0.84[MEX][hapmap]
rs2275620	0.81[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2275622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2860974	0.94[AFR][1000 genomes]
rs2860975	0.81[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap]
rs6583968	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6583969	0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7070074	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7077618	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7087256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100061	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7898759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910936	0.81[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9703851	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1035409	chr10:96495177-96832057	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1050544	chr10:96766934-96814689	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1044182	chr10:96783996-96814689	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv2761618	chr10:96784008-96814689	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Immune response to smallpox vaccine (IL-6)	22542470	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1934953	PPP1R3C	cis	parietal	SCAN
rs1934953	EXOSC1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96795000-96798200	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr10:96796200-96797600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:96796400-96805400	Strong transcription	Liver	Liver

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