Variant report

Variant	rs10259576
Chromosome Location	chr7:56644687-56644688
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10215049	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10215703	0.82[ASW][hapmap];0.90[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10215705	0.92[EUR][1000 genomes]
rs10224323	1.00[ASN][1000 genomes]
rs10226486	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226756	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232356	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232838	1.00[ASN][1000 genomes]
rs10235121	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs10236798	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10237408	1.00[ASN][1000 genomes]
rs10239401	1.00[ASN][1000 genomes]
rs10242086	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs10247589	1.00[ASN][1000 genomes]
rs10249023	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10256440	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266889	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269082	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272852	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281482	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282398	0.90[EUR][1000 genomes]
rs10282564	1.00[ASN][1000 genomes]
rs1105304	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105305	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105306	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976129	1.00[ASN][1000 genomes]
rs11977998	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155162	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155169	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534308	1.00[CHD][hapmap]
rs12535550	1.00[CHD][hapmap]
rs12719002	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs12719003	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13231784	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13242355	1.00[ASN][1000 genomes]
rs13243299	1.00[ASN][1000 genomes]
rs13245583	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13307736	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13312340	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352444	0.93[EUR][1000 genomes]
rs1387067	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532083	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1906626	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1906629	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135483	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34270096	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34340801	0.84[EUR][1000 genomes]
rs34593554	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34614916	1.00[ASN][1000 genomes]
rs34765785	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34774343	1.00[ASN][1000 genomes]
rs35043412	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35483986	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3749500	0.82[ASW][hapmap];0.90[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3828495	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4245580	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4285439	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4442091	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947553	0.90[EUR][1000 genomes]
rs56869388	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57448144	1.00[ASN][1000 genomes]
rs66831640	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67173162	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944931	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6952677	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952857	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955935	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957076	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957105	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959032	1.00[ASN][1000 genomes]
rs6968161	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968398	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357108	0.95[CEU][hapmap]
rs7458882	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782035	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7782889	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783143	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7785531	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7791803	1.00[ASN][1000 genomes]
rs7796117	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7804839	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9656713	0.93[EUR][1000 genomes]
rs9656714	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033163	chr7:56307057-56677865	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv538863	chr7:56307057-56677865	ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv427783	chr7:56334626-56983646	Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1022563	chr7:56383876-57318888	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1016255	chr7:56453095-56835595	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv888066	chr7:56466740-56693762	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1028678	chr7:56511649-56795206	ZNF genes & repeats Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv538864	chr7:56511649-56795206	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1020833	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv538865	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
11	nsv8090	chr7:56511877-56772523	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv1017561	chr7:56512618-57334136	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
13	nsv831009	chr7:56566629-56754313	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1030968	chr7:56610656-56835595	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription	TF binding region CpG island lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv5758	chr7:56637221-56705333	ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv966799	chr7:56643764-56660276	ZNF genes & repeats	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv508456	chr7:56644586-56664331	ZNF genes & repeats	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10259576	CHCHD2	cis	parietal	SCAN
rs10259576	SEPT14	cis	cerebellum	SCAN
rs10259576	LANCL2	cis	cerebellum	SCAN

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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