Variant report

Variant	rs12604069
Chromosome Location	chr17:19516216-19516217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1004490	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1004491	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1034897	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11204407	0.85[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11650399	0.86[CHD][hapmap]
rs12601634	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12940877	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12945345	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16960251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072332	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2120271	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28672254	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2891951	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34242564	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35364675	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3752046	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3786038	0.85[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4244600	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4621031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4646793	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4646800	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924788	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925000	0.81[EUR][1000 genomes]
rs4925001	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4925002	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925026	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925037	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925038	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4925041	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56262978	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58835440	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58970893	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61631401	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67870359	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68066777	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216938	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73981559	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7502080	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs962801	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs968012	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902636	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9909886	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9914765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:69 , 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	nsv817755	chr17:19494178-19517768	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv1065184	chr17:19494907-19524739	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
21	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
22	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
23	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
24	nsv1055165	chr17:19497569-19527596	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv1065379	chr17:19497890-19524335	Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
26	nsv1060623	chr17:19497890-19524739	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
27	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
28	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
29	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
30	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
31	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
32	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
33	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
34	nsv1057789	chr17:19499724-19524237	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
35	nsv1065681	chr17:19499724-19524721	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
36	nsv1057652	chr17:19499724-19524739	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
37	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
38	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
39	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
40	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
41	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
42	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
43	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
44	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
45	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
46	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
47	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
48	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
49	nsv960075	chr17:19501811-19517783	Enhancers Bivalent Enhancer Weak transcription	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
50	nsv1063316	chr17:19501943-19524739	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12604069	ALDH3A2	cis	multi-tissue	Pritchard
rs12604069	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19499800-19519000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:19515000-19518200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr17:19515800-19516800	Weak transcription	A549	lung

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