Variant report

Variant	rs28407129
Chromosome Location	chr14:104396669-104396670
allele	C/T
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	NR2F2	chr14:104396413-104397073	MCF-7	breast:	n/a	n/a
2	FOSL2	chr14:104396556-104396910	HepG2	liver:	n/a	n/a
3	TCF7L2	chr14:104396660-104396840	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr14:104396445-104397093	MCF-7	breast:	n/a	n/a
5	NR2F2	chr14:104396474-104397099	MCF-7	breast:	n/a	n/a
6	FOSL2	chr14:104396602-104396895	HepG2	liver:	n/a	n/a
7	ESR1	chr14:104396623-104396899	ECC-1	luminal epithelium:	n/a	chr14:104396732-104396747
8	ESR1	chr14:104396594-104396992	ECC-1	luminal epithelium:	n/a	chr14:104396732-104396747
9	JUND	chr14:104396646-104396893	HepG2	liver:	n/a	n/a
10	CEBPB	chr14:104396376-104397128	MCF-7	breast:	n/a	chr14:104396944-104396956
11	EP300	chr14:104396513-104396943	MCF-7	breast:	n/a	chr14:104396812-104396826
12	ESR1	chr14:104396545-104396956	T-47D	breast:	n/a	chr14:104396732-104396747
13	ESR1	chr14:104396501-104396851	ECC-1	luminal epithelium:	n/a	chr14:104396732-104396747
14	FOS	chr14:104396666-104396924	MCF10A-Er-Src	breast:	n/a	n/a
15	TCF7L2	chr14:104396650-104397025	MCF-7	breast:	n/a	n/a
16	EP300	chr14:104396501-104397114	MCF-7	breast:	n/a	chr14:104396812-104396826
17	FOS	chr14:104396612-104396947	MCF10A-Er-Src	breast:	n/a	n/a
18	FOSL2	chr14:104396500-104397065	MCF-7	breast:	n/a	n/a
19	ESR1	chr14:104396641-104396938	T-47D	breast:	n/a	chr14:104396732-104396747
20	ESR1	chr14:104396600-104396891	ECC-1	luminal epithelium:	n/a	chr14:104396732-104396747
21	ESR1	chr14:104396644-104396940	ECC-1	luminal epithelium:	n/a	chr14:104396732-104396747
22	STAT3	chr14:104396587-104396889	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:104159423..104160385-chr14:104396350..104397254,2	MCF-7	breast:
2	chr14:104391843..104393363-chr14:104396413..104398370,2	K562	blood:
3	chr14:104385710..104388983-chr14:104393675..104397966,4	MCF-7	breast:
4	chr14:104395726..104398249-chr14:104421446..104423004,2	K562	blood:
5	chr14:104393603..104397064-chr14:104407702..104410726,3	K562	blood:
6	chr14:104387945..104390196-chr14:104396396..104397958,2	MCF-7	breast:

Variant related genes	Relation type
C14orf2	TF binding region
ENSG00000156411	Chromatin interaction
ENSG00000227729	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10129730	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10131031	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10131231	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10137889	0.84[AMR][1000 genomes]
rs10139210	0.84[AMR][1000 genomes]
rs10142365	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10149898	0.84[AMR][1000 genomes]
rs12437404	0.90[ASN][1000 genomes]
rs17101922	1.00[ASN][1000 genomes]
rs17101932	1.00[EUR][1000 genomes]
rs1951580	1.00[EUR][1000 genomes]
rs1951587	1.00[EUR][1000 genomes]
rs2295662	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28432266	0.83[EUR][1000 genomes]
rs28439019	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28493894	1.00[ASN][1000 genomes]
rs28563863	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34606901	1.00[ASN][1000 genomes]
rs45471291	1.00[EUR][1000 genomes]
rs45540638	1.00[EUR][1000 genomes]
rs4900603	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4906384	1.00[ASN][1000 genomes]
rs4906386	1.00[ASN][1000 genomes]
rs4906388	0.84[AMR][1000 genomes]
rs55920546	0.90[ASN][1000 genomes]
rs56817754	1.00[ASN][1000 genomes]
rs57047619	1.00[EUR][1000 genomes]
rs57711557	1.00[EUR][1000 genomes]
rs58071582	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58557120	1.00[EUR][1000 genomes]
rs58701300	0.90[ASN][1000 genomes]
rs59838226	0.84[AMR][1000 genomes]
rs59945383	1.00[EUR][1000 genomes]
rs60080575	0.86[EUR][1000 genomes]
rs60532123	1.00[EUR][1000 genomes]
rs61451840	1.00[EUR][1000 genomes]
rs6576015	0.86[EUR][1000 genomes]
rs7144445	1.00[EUR][1000 genomes]
rs7156752	1.00[EUR][1000 genomes]
rs7157034	0.86[EUR][1000 genomes]
rs7158035	0.86[EUR][1000 genomes]
rs74086761	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74086762	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74086783	0.84[AMR][1000 genomes]
rs74089114	0.86[EUR][1000 genomes]
rs8004485	0.80[AMR][1000 genomes]
rs8009847	1.00[ASN][1000 genomes]
rs8020110	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8020476	0.86[EUR][1000 genomes]
rs8021647	0.86[EUR][1000 genomes]
rs8022184	0.86[EUR][1000 genomes]
rs8022769	1.00[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	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
7	nsv1048353	chr14:104361402-104483286	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv902322	chr14:104365310-104464809	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv902323	chr14:104381687-104464809	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104394600-104398200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:104395000-104401200	Weak transcription	Spleen	Spleen
3	chr14:104395400-104399400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr14:104395600-104397200	Enhancers	HepG2	liver
5	chr14:104395600-104398200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr14:104396200-104397000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr14:104396200-104397200	Enhancers	Primary B cells from cord blood	blood
8	chr14:104396200-104399800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr14:104396600-104399400	Weak transcription	Hela-S3	cervix
10	chr14:104396600-104400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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