Variant report

Variant	rs2860975
Chromosome Location	chr10:96766934-96766935
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10786182	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882514	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882516	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11188139	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11188141	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11188142	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188170	0.92[AFR][1000 genomes]
rs11572120	0.82[AFR][1000 genomes]
rs12358804	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1341163	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1579029	0.92[AFR][1000 genomes]
rs1891071	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1891073	0.81[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs1934953	0.81[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs1934973	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1934979	0.89[AFR][1000 genomes]
rs1934985	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2275620	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2275622	0.87[CHB][hapmap]
rs2860974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6583968	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7070074	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7077618	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7087256	0.94[AFR][1000 genomes]
rs7095531	0.81[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs7898759	0.94[AFR][1000 genomes]
rs7910936	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

Variant related diseases (count:1)

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2860975	PPP1R3C	cis	parietal	SCAN
rs2860975	EXOSC1	cis	cerebellum	SCAN
rs2860975	TCTN3	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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