Variant report

Variant	rs12713227
Chromosome Location	chr2:53090018-53090019
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	FOS	chr2:53089862-53090311	MCF10A-Er-Src	breast:	n/a	chr2:53090034-53090043
2	CEBPB	chr2:53089862-53090309	A549	lung:	n/a	chr2:53090036-53090044
3	STAT3	chr2:53089904-53090285	MCF10A-Er-Src	breast:	n/a	chr2:53090130-53090139 chr2:53090131-53090140
4	FOSL1	chr2:53089914-53090419	HCT-116	colon:	n/a	chr2:53090034-53090043
5	EP300	chr2:53089825-53090361	A549	lung:	n/a	n/a
6	FOS	chr2:53089817-53090312	MCF10A-Er-Src	breast:	n/a	chr2:53090034-53090043
7	FOS	chr2:53089953-53090275	MCF10A-Er-Src	breast:	n/a	chr2:53090034-53090043
8	STAT3	chr2:53090015-53090232	MCF10A-Er-Src	breast:	n/a	chr2:53090130-53090139 chr2:53090131-53090140
9	GATA3	chr2:53089763-53090368	A549	lung:	n/a	chr2:53090311-53090318
10	TEAD4	chr2:53089941-53090316	HCT-116	colon:	n/a	n/a
11	FOSL2	chr2:53089855-53090313	A549	lung:	n/a	chr2:53090034-53090043
12	EP300	chr2:53089930-53090244	Hela-S3	cervix:	n/a	n/a
13	TEAD4	chr2:53090016-53090266	A549	lung:	n/a	n/a
14	FOSL2	chr2:53089967-53090291	A549	lung:	n/a	chr2:53090034-53090043
15	SP1	chr2:53089815-53090476	HCT-116	colon:	n/a	n/a
16	SP1	chr2:53089921-53090352	A549	lung:	n/a	n/a
17	FOS	chr2:53089963-53090297	MCF10A-Er-Src	breast:	n/a	chr2:53090034-53090043
18	SP1	chr2:53089857-53090428	A549	lung:	n/a	n/a
19	FOSL1	chr2:53089892-53090397	HCT-116	colon:	n/a	chr2:53090034-53090043
20	STAT3	chr2:53089827-53090325	MCF10A-Er-Src	breast:	n/a	chr2:53090130-53090139 chr2:53090131-53090140
21	TCF12	chr2:53089859-53090964	A549	lung:	n/a	chr2:53090593-53090602
22	JUND	chr2:53089837-53090386	HCT-116	colon:	n/a	chr2:53090034-53090043
23	JUND	chr2:53089962-53090384	HCT-116	colon:	n/a	chr2:53090034-53090043
24	TEAD4	chr2:53089963-53090279	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
ENSG00000232604	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10164801	0.91[EUR][1000 genomes]
rs10164868	0.90[EUR][1000 genomes]
rs10167421	0.91[EUR][1000 genomes]
rs10168840	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10173886	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10179810	0.91[EUR][1000 genomes]
rs10184255	0.81[EUR][1000 genomes]
rs10187465	0.95[CHB][hapmap]
rs10191273	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10203699	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10206560	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs10208858	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865272	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12475542	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12477231	0.93[EUR][1000 genomes]
rs12614959	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs12617374	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12617738	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12618983	0.93[EUR][1000 genomes]
rs12713228	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs12713229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713230	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs12713231	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713232	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs12713233	0.90[EUR][1000 genomes]
rs12990843	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs13002328	0.93[EUR][1000 genomes]
rs13003962	0.92[EUR][1000 genomes]
rs13030509	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13387682	0.92[CEU][hapmap]
rs1376563	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1376567	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1376569	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1376570	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1451455	0.91[EUR][1000 genomes]
rs1451456	0.93[EUR][1000 genomes]
rs1451458	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1451459	0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1451460	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1542282	0.83[ASN][1000 genomes]
rs1597653	0.91[EUR][1000 genomes]
rs1597654	0.87[ASN][1000 genomes]
rs17504530	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1828337	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1828338	0.86[EUR][1000 genomes]
rs1839770	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1839771	0.90[EUR][1000 genomes]
rs1864534	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2356680	0.92[EUR][1000 genomes]
rs2356681	0.91[EUR][1000 genomes]
rs36130286	0.84[EUR][1000 genomes]
rs4143203	0.82[EUR][1000 genomes]
rs4525730	0.92[EUR][1000 genomes]
rs6545310	0.92[EUR][1000 genomes]
rs6715847	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6715857	0.92[EUR][1000 genomes]
rs6725912	0.92[EUR][1000 genomes]
rs6730735	0.89[ASN][1000 genomes]
rs6737483	0.81[EUR][1000 genomes]
rs6746666	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6754205	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754423	0.92[EUR][1000 genomes]
rs67939368	0.92[EUR][1000 genomes]
rs724859	0.91[EUR][1000 genomes]
rs724860	0.91[EUR][1000 genomes]
rs74181216	0.93[EUR][1000 genomes]
rs7577692	0.92[EUR][1000 genomes]
rs7582787	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998380	chr2:52891706-53222155	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	esv2763631	chr2:52910862-53169629	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006244	chr2:52958322-53169617	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1005813	chr2:52959769-53114865	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1010978	chr2:52959769-53249951	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1014068	chr2:52960353-53169617	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv520722	chr2:53039770-53421015	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3435550	chr2:53069350-53092313	Weak transcription Enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
9	nsv1010237	chr2:53072736-53116413	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53085800-53090600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:53088600-53090400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:53089400-53090200	Enhancers	A549	lung
4	chr2:53089800-53090200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:53089800-53090200	Weak transcription	NHDF-Ad	bronchial

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