Variant report

Variant	rs12902050
Chromosome Location	chr15:51085374-51085375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51055876..51059708-chr15:51082487..51085747,5	MCF-7	breast:
2	chr15:51083211..51087261-chr15:51087532..51090501,5	MCF-7	breast:
3	chr15:51057652..51059901-chr15:51083890..51085609,2	K562	blood:

Variant related genes	Relation type
ENSG00000138600	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10152336	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10153007	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070814	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070825	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11854559	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11855675	0.95[ASN][1000 genomes]
rs11856129	0.81[ASN][1000 genomes]
rs11857981	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12324214	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324583	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12441734	0.88[JPT][hapmap]
rs12898402	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12899528	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906278	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907367	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12909351	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12909780	0.81[ASN][1000 genomes]
rs12910301	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12911270	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12913094	0.91[JPT][hapmap]
rs12914364	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915836	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916255	0.94[JPT][hapmap]
rs12916608	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916630	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16953045	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs16963879	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963910	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16963912	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16963947	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17521467	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17599863	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17599974	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1904432	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1912097	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2414053	0.95[ASN][1000 genomes]
rs2414054	0.95[ASN][1000 genomes]
rs2414055	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2414056	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28566562	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28580166	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28719095	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28796723	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28858690	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899459	0.95[ASN][1000 genomes]
rs34293575	0.90[ASN][1000 genomes]
rs34297767	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34575622	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34581168	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34676299	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34805236	1.00[AFR][1000 genomes]
rs35019442	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35073878	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355541	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35464909	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35821307	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35845857	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816717	0.94[JPT][hapmap]
rs3848133	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3848134	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3848135	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3891815	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3896066	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3925824	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3929486	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131085	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4344678	0.95[ASN][1000 genomes]
rs4402498	0.95[ASN][1000 genomes]
rs4451894	0.95[ASN][1000 genomes]
rs6493455	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493458	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6493459	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493470	0.94[JPT][hapmap]
rs71471516	0.95[ASN][1000 genomes]
rs71471517	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71471518	0.91[ASN][1000 genomes]
rs7162325	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7162631	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166073	0.81[TSI][hapmap]
rs7169887	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7170364	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7170937	0.85[CHD][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172667	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175024	1.00[JPT][hapmap]
rs7179321	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7179865	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8023655	0.91[ASN][1000 genomes]
rs8024423	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8024689	0.95[ASN][1000 genomes]
rs8024733	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027547	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8029786	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8032866	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8033015	0.83[JPT][hapmap]
rs8033085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8033307	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8033351	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8033471	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034303	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034718	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034918	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036604	0.94[JPT][hapmap]
rs8038437	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9302158	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9630423	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9806247	0.95[ASN][1000 genomes]
rs9806654	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1051990	chr15:50745814-51133186	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv457134	chr15:50770868-51184583	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv471242	chr15:50770868-51184583	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv569396	chr15:50770868-51184583	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	nsv457135	chr15:50770868-51189707	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
11	nsv569397	chr15:50770868-51189707	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv1048621	chr15:50775451-51115535	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv1047039	chr15:50782070-51187804	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv542385	chr15:50782070-51187804	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
15	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
16	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
17	nsv1036081	chr15:50818569-51097229	Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
18	nsv1055112	chr15:50822035-51133186	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	nsv1042372	chr15:50846461-51208891	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
20	nsv542386	chr15:50846461-51208891	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
21	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
22	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
23	nsv904212	chr15:50979738-51132170	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
24	nsv904213	chr15:51011402-51119731	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	nsv457137	chr15:51019117-51117524	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
26	nsv569402	chr15:51019117-51117524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
27	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
28	esv15453	chr15:51072875-51086217	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12902050	DUOXA2	cis	cerebellum	SCAN
rs12902050	AP4E1	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51079200-51091000	Weak transcription	HepG2	liver
2	chr15:51080400-51090200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr15:51082200-51085400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr15:51082600-51085400	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr15:51082600-51090800	Weak transcription	K562	blood
6	chr15:51084400-51090200	Weak transcription	Fetal Intestine Large	intestine
7	chr15:51084600-51089200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:51084800-51086400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:51085000-51087200	Weak transcription	Colonic Mucosa	Colon

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