Variant report

Variant	rs6587200
Chromosome Location	chr17:19526125-19526126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11656199	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11656773	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11871420	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150145	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12941194	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17684040	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2108971	0.89[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2120274	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2165895	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2245639	0.87[EUR][1000 genomes]
rs2386143	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2386145	0.89[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2440162	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2453586	0.87[EUR][1000 genomes]
rs2453600	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2453601	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2453604	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2453608	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28495827	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3760489	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925036	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs56109259	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62065943	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62065946	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6587201	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7210433	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7215	0.88[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7405861	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7405862	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7502992	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8069478	0.82[EUR][1000 genomes]
rs8069576	0.89[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8074500	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8074784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8079648	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8081130	0.86[MEX][hapmap]
rs962800	0.89[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9889632	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9903027	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:58 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1056125	chr17:19484803-19536116	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1059195	chr17:19484803-19547972	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription 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	35 gene(s)	inside rSNPs	diseases
8	nsv437815	chr17:19488851-19545834	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv437816	chr17:19488851-19545834	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1058163	chr17:19492744-19536116	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv3693233	chr17:19494178-19537470	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv574575	chr17:19494756-19534434	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1061056	chr17:19494805-19534994	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1056780	chr17:19494805-19537470	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1055871	chr17:19494805-19538435	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2760461	chr17:19494817-19538758	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1056466	chr17:19494855-19537470	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv1059269	chr17:19494855-19538435	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv1060819	chr17:19494907-19538746	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv574576	chr17:19495478-19534434	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv870221	chr17:19497302-19546080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv1055165	chr17:19497569-19527596	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv1059515	chr17:19497890-19537470	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1065299	chr17:19497890-19538435	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv1060185	chr17:19497890-19538746	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
26	esv2762555	chr17:19497890-19538758	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
27	nsv1061339	chr17:19497890-19543162	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
28	esv3315172	chr17:19498590-19538709	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
29	esv3315173	chr17:19498590-19538709	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
30	nsv1064221	chr17:19499724-19534994	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
31	nsv1062843	chr17:19499724-19537470	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
32	nsv1058837	chr17:19499724-19538435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
33	nsv1056213	chr17:19499724-19538746	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
34	nsv1058288	chr17:19499724-19543162	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
35	nsv1059856	chr17:19499724-19543186	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
36	nsv1062609	chr17:19499724-19543361	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
37	nsv1064603	chr17:19499724-19544138	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
38	nsv1064042	chr17:19499724-19544277	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
39	esv2421703	chr17:19499736-19538447	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
40	nsv442739	chr17:19499736-19538447	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
41	nsv514829	chr17:19500192-19537612	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
42	nsv1061005	chr17:19501943-19537470	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
43	nsv1056853	chr17:19501943-19538435	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
44	nsv1063775	chr17:19501943-19538746	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
45	nsv1063104	chr17:19501943-19543162	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
46	nsv574577	chr17:19505984-19546100	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
47	nsv1067315	chr17:19513698-19538435	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
48	nsv1064779	chr17:19513751-19538746	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
49	nsv543254	chr17:19515267-19527596	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases
50	nsv543255	chr17:19515267-19536116	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6587200	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19525400-19538800	Weak transcription	Ovary	ovary

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