Variant report

Variant	rs12898430
Chromosome Location	chr15:76874923-76874924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr15:76874910-76875249	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
MIR3713	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10444858	0.82[ASN][1000 genomes]
rs11072603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117367	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125932	0.85[ASN][1000 genomes]
rs12148452	0.82[ASN][1000 genomes]
rs12148786	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148805	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12437627	0.90[ASN][1000 genomes]
rs12438077	0.90[ASN][1000 genomes]
rs12441247	0.85[ASN][1000 genomes]
rs12441433	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441550	0.90[ASN][1000 genomes]
rs12443137	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594212	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594541	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594577	0.85[ASN][1000 genomes]
rs12595313	0.82[ASN][1000 genomes]
rs12902174	0.90[ASN][1000 genomes]
rs12908421	0.89[ASN][1000 genomes]
rs1838050	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1874944	0.90[ASN][1000 genomes]
rs1946650	0.90[ASN][1000 genomes]
rs2056544	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2083762	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2120107	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120108	0.91[ASN][1000 genomes]
rs2304920	0.82[ASN][1000 genomes]
rs2404602	0.81[ASN][1000 genomes]
rs2404736	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2404737	0.91[ASN][1000 genomes]
rs2404740	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404741	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2896954	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34060246	0.82[ASN][1000 genomes]
rs34707035	0.82[ASN][1000 genomes]
rs34924128	0.82[ASN][1000 genomes]
rs35138393	0.82[ASN][1000 genomes]
rs35395069	0.82[ASN][1000 genomes]
rs35498563	0.82[ASN][1000 genomes]
rs35566346	0.87[ASN][1000 genomes]
rs3816266	0.82[ASN][1000 genomes]
rs4886496	0.88[ASN][1000 genomes]
rs4886813	0.85[ASN][1000 genomes]
rs4886817	0.91[ASN][1000 genomes]
rs4886818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886824	0.81[ASN][1000 genomes]
rs4886825	0.82[ASN][1000 genomes]
rs55676827	0.82[ASN][1000 genomes]
rs56351018	0.85[ASN][1000 genomes]
rs58361452	0.82[ASN][1000 genomes]
rs58511211	0.85[ASN][1000 genomes]
rs58973160	0.82[ASN][1000 genomes]
rs59088060	0.90[ASN][1000 genomes]
rs60912217	0.80[ASN][1000 genomes]
rs6495206	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66754747	0.85[ASN][1000 genomes]
rs67010831	0.82[ASN][1000 genomes]
rs67204011	0.90[ASN][1000 genomes]
rs67570291	0.82[ASN][1000 genomes]
rs71405216	0.87[ASN][1000 genomes]
rs71405223	0.82[ASN][1000 genomes]
rs7167613	0.82[ASN][1000 genomes]
rs72738889	0.82[ASN][1000 genomes]
rs7342603	0.82[ASN][1000 genomes]
rs7350777	0.82[ASN][1000 genomes]
rs8024476	0.82[ASN][1000 genomes]
rs8043474	0.82[ASN][1000 genomes]
rs9646213	0.84[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	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1042514	chr15:76838221-76906382	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1038233	chr15:76855205-76895763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1037282	chr15:76859309-76895763	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1044453	chr15:76860198-76895763	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1620	chr15:76862152-76914288	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
16	nsv904402	chr15:76863023-76930805	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
17	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1048577	chr15:76868215-76895763	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
21	nsv1051037	chr15:76868215-76902257	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1038521	chr15:76869789-76895763	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
23	nsv1042304	chr15:76869929-76895763	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
24	esv3584695	chr15:76869929-76895775	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1042883	chr15:76869929-76902458	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
26	nsv904403	chr15:76869929-76951040	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
27	nsv904404	chr15:76869929-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
28	nsv904405	chr15:76869929-77047915	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
29	nsv904406	chr15:76869929-77085283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
30	nsv904407	chr15:76869929-77121196	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12898430	SCAPER	cis	Esophagus Mucosa	GTEx
rs12898430	SCAPER	cis	Thyroid	GTEx
rs12898430	SCAPER	cis	Artery Tibial	GTEx
rs12898430	SCAPER	cis	lung	GTEx
rs12898430	SCAPER	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76869400-76881200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:76870400-76876000	Weak transcription	Right Ventricle	heart
3	chr15:76870400-76881200	Weak transcription	Lung	lung
4	chr15:76871000-76883600	Weak transcription	Ovary	ovary
5	chr15:76874200-76881600	Weak transcription	Esophagus	oesophagus

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