Variant report

Variant	rs9288959
Chromosome Location	chr3:112548580-112548581
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10804504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10804505	0.83[ASN][1000 genomes]
rs10804506	0.98[AFR][1000 genomes]
rs10934188	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934191	0.83[ASN][1000 genomes]
rs1114404	0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11717778	0.83[ASN][1000 genomes]
rs12489734	0.84[CEU][hapmap];0.83[ASN][1000 genomes]
rs12695270	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13063847	0.83[ASN][1000 genomes]
rs13094280	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13100559	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1997281	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs28782232	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6763318	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs6765575	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6786513	0.82[ASN][1000 genomes]
rs6787688	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap]
rs6806976	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6808135	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7609699	0.91[AFR][1000 genomes]
rs7621490	0.82[ASN][1000 genomes]
rs7651207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288958	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288964	0.98[AFR][1000 genomes]
rs9809444	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9810246	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814008	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9823692	0.95[AFR][1000 genomes]
rs9826834	0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9829184	0.83[ASN][1000 genomes]
rs9834599	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9839592	0.95[AFR][1000 genomes]
rs9842637	0.83[ASN][1000 genomes]
rs9865066	0.83[ASN][1000 genomes]
rs9871326	0.88[AFR][1000 genomes]
rs9871605	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs9879005	0.83[JPT][hapmap]

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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3501334	chr3:112546820-112648766	Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3501335	chr3:112546820-112648766	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9288959	C3orf17	cis	cerebellum	SCAN
rs9288959	SLC9A10	cis	parietal	SCAN
rs9288959	ABHD10	cis	cerebellum	SCAN
rs9288959	CD200R1	cis	multi-tissue	Pritchard

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

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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