Variant report

Variant	rs28672254
Chromosome Location	chr17:19535920-19535921
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19528725..19530470-chr17:19534495..19536172,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004490	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1004491	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1034897	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11204407	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12601634	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12604069	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12940877	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945345	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16960251	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072332	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2120271	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891951	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364675	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3752046	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3786038	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4244600	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4621031	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646793	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646800	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924788	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924791	0.83[AMR][1000 genomes]
rs4925001	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925002	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925026	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925037	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925038	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925040	0.82[AMR][1000 genomes]
rs4925041	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56262978	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58835440	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58970893	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61631401	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67870359	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68066777	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216938	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73981559	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7502080	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs962801	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs968012	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9902636	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9909886	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9914765	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:51 , 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	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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
33	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
34	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
35	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
36	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
37	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
38	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
39	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
40	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
41	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
42	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
43	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
44	nsv543255	chr17:19515267-19536116	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
45	nsv543256	chr17:19515267-19547972	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
46	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
47	nsv457701	chr17:19515695-19537470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
48	nsv457702	chr17:19515695-19537470	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
49	nsv457703	chr17:19515695-19537470	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
50	nsv574578	chr17:19515695-19537470	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28672254	ALDH3A2	cis	multi-tissue	Pritchard
rs28672254	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19525400-19538800	Weak transcription	Ovary	ovary
2	chr17:19529800-19538200	Weak transcription	Liver	Liver
3	chr17:19533200-19536600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr17:19534400-19545400	Weak transcription	A549	lung
5	chr17:19534800-19536800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr17:19535200-19536000	Enhancers	HepG2	liver
7	chr17:19535400-19536400	Enhancers	Small Intestine	intestine
8	chr17:19535600-19536000	Enhancers	Fetal Intestine Small	intestine

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