Variant report

Variant	rs2414561
Chromosome Location	chr15:58551444-58551445
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	STAT3	chr15:58550843-58551734	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr15:58551150-58551465	Hela-S3	cervix:	n/a	n/a
3	FOS	chr15:58551000-58551487	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr15:58550964-58551549	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr15:58551117-58551512	Hela-S3	cervix:	n/a	n/a
6	STAT3	chr15:58550749-58551549	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr15:58551008-58551504	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr15:58550245-58553629	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr15:58550817-58551485	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr15:58550918-58551618	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr15:58551062-58551474	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:58550148-58552138	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr15:58551079-58551532	Hela-S3	cervix:	n/a	n/a
14	EP300	chr15:58551104-58551456	Hela-S3	cervix:	n/a	n/a
15	FOS	chr15:58551073-58551561	MCF10A-Er-Src	breast:	n/a	n/a
16	USF2	chr15:58551111-58551504	Hela-S3	cervix:	n/a	n/a
17	STAT3	chr15:58551023-58551608	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr15:58551007-58551590	MCF10A-Er-Src	breast:	n/a	n/a
19	MAX	chr15:58551081-58551532	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58549388..58551479-chr15:59062229..59064301,2	K562	blood:

Variant related genes	Relation type
ALDH1A2	TF binding region
ENSG00000245975	Chromatin interaction
ENSG00000128923	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12592326	0.82[CEU][hapmap];0.89[AMR][1000 genomes]
rs12899324	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12904030	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1663260	0.87[AMR][1000 genomes]
rs16939991	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17240685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1814867	0.82[AMR][1000 genomes]
rs2414563	0.87[AMR][1000 genomes]
rs34149555	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34458264	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35348919	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36045724	0.87[AMR][1000 genomes]
rs4542601	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62000520	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493993	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7164378	0.81[CEU][hapmap];0.89[AMR][1000 genomes]
rs7173510	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178337	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178779	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179597	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179726	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7181607	0.89[AMR][1000 genomes]
rs7183294	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033046	0.89[AMR][1000 genomes]
rs8040159	0.83[AMR][1000 genomes]
rs8042351	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[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	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv833024	chr15:58447459-58621963	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1050473	chr15:58479888-58562270	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv904264	chr15:58505122-58588510	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv904265	chr15:58517528-58588510	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS 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	50 gene(s)	inside rSNPs	diseases
7	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking 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	50 gene(s)	inside rSNPs	diseases
8	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58541000-58552800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:58547000-58552800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:58547800-58557000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:58548200-58552600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:58549600-58552400	Enhancers	Hela-S3	cervix
6	chr15:58549600-58558600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:58549800-58552200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr15:58550000-58551800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:58550000-58552400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr15:58550200-58551800	Weak transcription	K562	blood
11	chr15:58550200-58554000	Enhancers	HMEC	breast
12	chr15:58550400-58551800	Weak transcription	Placenta	Placenta
13	chr15:58550400-58551800	Weak transcription	Psoas Muscle	Psoas
14	chr15:58550400-58552800	Weak transcription	Left Ventricle	heart
15	chr15:58550400-58561800	Weak transcription	Liver	Liver
16	chr15:58550800-58551800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:58551000-58552200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:58551000-58553400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr15:58551000-58553400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr15:58551000-58553600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr15:58551200-58551600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr15:58551200-58551600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:58551200-58552000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:58551200-58552200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:58551200-58552400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr15:58551200-58552400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:58551200-58552600	Enhancers	NHEK	skin
28	chr15:58551200-58553600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr15:58551400-58552400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:58551400-58552400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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