Variant report

Variant	rs3007690
Chromosome Location	chr1:151927676-151927677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1003107	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs10158030	0.82[ASW][hapmap];1.00[CHB][hapmap]
rs1038746	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1038748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10788813	1.00[CHB][hapmap]
rs10788816	1.00[CHB][hapmap]
rs10888450	0.88[ASN][1000 genomes]
rs10888451	0.88[ASN][1000 genomes]
rs10888453	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11204911	1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs11204912	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11204923	0.82[CEU][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1352654	0.93[CHD][hapmap];0.90[GIH][hapmap];0.88[ASN][1000 genomes]
rs1387834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1387835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1473493	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1473494	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1473495	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1490187	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1490190	0.82[AMR][1000 genomes]
rs1490191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496037	1.00[CHB][hapmap]
rs1532132	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1552605	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1552606	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs1552607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1602245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602246	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1602248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17583707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1826170	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1826171	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1826172	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1844542	0.85[AMR][1000 genomes]
rs1873311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1873312	1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]
rs1967085	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs2087550	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2338018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2338210	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2932563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932564	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932567	1.00[CHB][hapmap]
rs2932578	0.82[AMR][1000 genomes]
rs2932584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932588	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932591	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932595	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932596	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932597	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999509	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2999511	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999515	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999518	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999519	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999520	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999522	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999523	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2999524	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999525	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999527	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999530	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2999535	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs2999538	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs2999551	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999555	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2999558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3001979	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007676	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007679	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007682	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3007692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007693	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3007699	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3007700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3007701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3007704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3122300	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3122301	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3134814	1.00[CHB][hapmap]
rs34370890	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845385	1.00[CHB][hapmap]
rs4845388	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs4845393	1.00[CHB][hapmap]
rs4845660	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs4845664	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs61113720	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6587626	1.00[CHB][hapmap]
rs6587628	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs6587629	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs6587630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6587641	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs6659029	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs6678664	0.91[ASN][1000 genomes]
rs6685291	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs6691350	1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]
rs7529451	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[MEX][hapmap]
rs7532721	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7544380	0.83[ASN][1000 genomes]
rs7545863	0.83[ASN][1000 genomes]
rs902314	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs902315	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs902316	0.88[ASN][1000 genomes]
rs959945	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs971888	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9943225	1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3007690	VPS72	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151926200-151927800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:151927200-151928000	Enhancers	Fetal Intestine Large	intestine
3	chr1:151927400-151928000	Enhancers	Fetal Intestine Small	intestine

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