Variant report

Variant	rs12940877
Chromosome Location	chr17:19543397-19543398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC47A2-2	chr17:19542441-19543431	XLOC_012417

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1004490	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1004491	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1034897	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11204407	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12601634	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12604069	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12945345	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16960251	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072332	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2120271	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28672254	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891951	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34242564	0.81[EUR][1000 genomes]
rs35364675	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3752046	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3786038	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4244600	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4621031	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646793	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4646800	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4924788	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924791	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4925000	0.81[EUR][1000 genomes]
rs4925001	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925002	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925026	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925037	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925038	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4925040	0.84[AMR][1000 genomes]
rs4925041	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56262978	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58835440	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58970893	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61631401	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67870359	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68066777	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216938	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73981559	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7502080	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs962801	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs968012	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9902636	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9909886	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9914765	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv574579	chr17:19515695-19546100	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv2558706	chr17:19542615-19544308	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv3365269	chr17:19542710-19544708	Enhancers Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv2107222	chr17:19543232-19543932	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
19	esv3530031	chr17:19543314-19543829	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv3355092	chr17:19543320-19543819	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
21	esv3530032	chr17:19543323-19543838	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
22	esv3530027	chr17:19543330-19543767	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
23	esv3530028	chr17:19543347-19543769	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
24	esv3314593	chr17:19543358-19543796	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
25	esv3314594	chr17:19543363-19543769	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
26	esv3314592	chr17:19543369-19543753	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
27	esv4573	chr17:19543369-19543844	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
28	esv3530033	chr17:19543371-19543786	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
29	esv3530026	chr17:19543380-19543777	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases
30	esv3385238	chr17:19543393-19543759	Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12940877	ALDH3A2	cis	multi-tissue	Pritchard
rs12940877	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19534400-19545400	Weak transcription	A549	lung
2	chr17:19536000-19545600	Weak transcription	HepG2	liver
3	chr17:19538000-19549400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:19538800-19544400	Weak transcription	Liver	Liver

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