Variant report

Variant	rs605253
Chromosome Location	chr15:42377744-42377745
allele	C/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	POLR2A	chr15:42377425-42377774	Hela-S3	cervix:	n/a	n/a
2	FOS	chr15:42376726-42377799	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr15:42377576-42377792	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr15:42377589-42377850	MCF10A-Er-Src	breast:	n/a	n/a
5	BHLHE40	chr15:42377526-42377785	HepG2	liver:	n/a	n/a
6	STAT3	chr15:42377586-42377767	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr15:42377592-42377773	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr15:42376672-42377850	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42358545..42359423-chr15:42377294..42378091,3	MCF-7	breast:

Variant related genes	Relation type
PLA2G4D	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1668571	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1668585	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1668589	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1668596	0.87[CEU][hapmap];0.89[CHB][hapmap];0.89[EUR][1000 genomes]
rs1712430	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs1712435	0.87[CEU][hapmap];0.89[CHB][hapmap];0.89[EUR][1000 genomes]
rs600415	0.89[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs614215	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs681811	0.90[ASN][1000 genomes]
rs776688	0.89[CHB][hapmap]
rs776689	0.90[CHB][hapmap]
rs776691	0.89[CHB][hapmap]
rs776696	0.84[CHB][hapmap];0.87[EUR][1000 genomes]
rs776702	0.91[EUR][1000 genomes]
rs776726	0.86[YRI][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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 miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1043641	chr15:42336584-42381240	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv904131	chr15:42343794-42390223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42369800-42385000	Weak transcription	Right Atrium	heart
2	chr15:42371800-42380800	Weak transcription	Pancreas	Pancrea
3	chr15:42372800-42383000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:42373400-42384400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:42373400-42384400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:42375000-42378200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:42375200-42380200	Weak transcription	Gastric	stomach
8	chr15:42375800-42377800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:42376400-42378200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr15:42376600-42378200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr15:42376600-42378600	Enhancers	Fetal Thymus	thymus
12	chr15:42376800-42378000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr15:42376800-42378000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:42376800-42378200	Enhancers	HMEC	breast
15	chr15:42376800-42384400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:42377000-42377800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr15:42377000-42377800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:42377000-42378400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:42377000-42381000	Weak transcription	Fetal Heart	heart
20	chr15:42377200-42378000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:42377200-42378000	Enhancers	NHEK	skin
22	chr15:42377200-42378200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:42377200-42381200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:42377400-42377800	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr15:42377400-42381000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:42377400-42382400	Weak transcription	Fetal Intestine Large	intestine
27	chr15:42377400-42384800	Weak transcription	Esophagus	oesophagus
28	chr15:42377600-42377800	Enhancers	Hela-S3	cervix
29	chr15:42377600-42378000	Bivalent Enhancer	HepG2	liver
30	chr15:42377600-42380800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:42377600-42381000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:42377600-42381400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:42377600-42383000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:42377600-42384800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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