Variant report

Variant	rs10198799
Chromosome Location	chr2:77290690-77290691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10174161	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10181919	0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap]
rs10187466	0.85[YRI][hapmap]
rs10192262	0.85[YRI][hapmap]
rs10201530	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs10520176	0.82[YRI][hapmap]
rs11126576	0.85[YRI][hapmap]
rs11126580	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11126582	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11126583	0.84[EUR][1000 genomes]
rs11126586	0.87[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs11126588	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11126589	0.91[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.81[EUR][1000 genomes]
rs11889639	0.81[EUR][1000 genomes]
rs11892997	0.82[TSI][hapmap]
rs11896560	0.85[YRI][hapmap]
rs11903423	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs12614582	0.83[EUR][1000 genomes]
rs12621674	0.80[JPT][hapmap]
rs13385651	0.82[YRI][hapmap]
rs13385727	0.85[YRI][hapmap]
rs13388459	0.82[TSI][hapmap]
rs13412552	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs13421983	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13422002	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13431979	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1374395	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1921733	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1997468	0.85[YRI][hapmap]
rs2860082	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2860940	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2860941	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28739330	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4455181	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4853283	0.85[YRI][hapmap]
rs56050325	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56120121	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56125553	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56242614	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56356710	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56357290	0.81[EUR][1000 genomes]
rs6547104	0.82[YRI][hapmap]
rs6547121	0.91[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap]
rs6719689	0.85[YRI][hapmap]
rs6725731	0.90[CHB][hapmap]
rs6730095	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs6746253	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6750737	0.87[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.81[MKK][hapmap]
rs6750865	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs715280	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7422204	0.85[YRI][hapmap]
rs7563917	0.80[JPT][hapmap]
rs7570003	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7583894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7586363	0.85[YRI][hapmap]
rs7599837	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs9309508	0.85[YRI][hapmap]
rs9309509	0.85[YRI][hapmap]
rs957839	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv997284	chr2:77233426-77303198	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1014895	chr2:77263452-77414507	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv874331	chr2:77264354-77305123	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
5	nsv458285	chr2:77276201-77345491	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases
6	nsv582252	chr2:77276201-77345491	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
7	nsv874332	chr2:77288585-77387208	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10198799	LOXL3	cis	cerebellum	SCAN
rs10198799	USF1	trans	parietal	SCAN

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

No data

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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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