Variant report

Variant	rs12904035
Chromosome Location	chr15:31326789-31326790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:31326246-31326810	MCF-7	breast:	n/a	n/a
2	GATA3	chr15:31326327-31326925	MCF-7	breast:	n/a	chr15:31326874-31326885
3	RAD21	chr15:31326470-31326801	ECC-1	luminal epithelium:	n/a	n/a
4	RAD21	chr15:31326504-31326793	HepG2	liver:	n/a	n/a
5	CTCF	chr15:31326480-31326853	MCF-7	breast:	n/a	n/a
6	RAD21	chr15:31326307-31326848	MCF-7	breast:	n/a	n/a
7	RAD21	chr15:31326365-31326825	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr15:31326360-31326943	MCF-7	breast:	n/a	n/a
9	CTCF	chr15:31326700-31326850	HepG2	liver:	n/a	n/a
10	CTCF	chr15:31326529-31326803	MCF-7	breast:	n/a	n/a
11	GATA3	chr15:31326290-31326834	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr15:31326159-31326961	MCF-7	breast:	n/a	n/a
13	CTCF	chr15:31326556-31326789	GM19240	blood:	n/a	n/a
14	CTCF	chr15:31326700-31326850	AG04450	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31326150..31329950-chr15:31331273..31334217,4	MCF-7	breast:
2	chr15:31322324..31324539-chr15:31326738..31328309,2	K562	blood:

No data

Variant related genes	Relation type
TRPM1	TF binding region
ENSG00000134160	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10162706	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10162957	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12708421	0.83[ASN][1000 genomes]
rs12907509	0.83[ASN][1000 genomes]
rs12908432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12911350	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12913672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12914747	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12917058	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16956509	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17228080	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17815780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28480303	0.83[ASN][1000 genomes]
rs2911855	1.00[CHB][hapmap]
rs34969393	0.83[ASN][1000 genomes]
rs3784594	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3784595	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs61997150	0.83[ASN][1000 genomes]
rs7167823	0.83[ASN][1000 genomes]
rs7179148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8039189	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
8	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
12	nsv903835	chr15:31312743-31384797	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12904035	SNORD115-25	cis	cerebellum	SCAN
rs12904035	KLF13	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31316800-31330000	Weak transcription	Pancreas	Pancrea
2	chr15:31317400-31328400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:31317400-31334200	Weak transcription	Gastric	stomach
4	chr15:31323200-31326800	Enhancers	HUVEC	blood vessel
5	chr15:31323200-31326800	Enhancers	NHDF-Ad	bronchial
6	chr15:31324600-31326800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:31324800-31326800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:31324800-31326800	Enhancers	Lung	lung
9	chr15:31324800-31328000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:31324800-31332600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:31324800-31332800	Enhancers	Placenta	Placenta
12	chr15:31325400-31326800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:31325400-31326800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr15:31325400-31328800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:31325600-31326800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:31325600-31326800	Enhancers	Esophagus	oesophagus
17	chr15:31325600-31327600	Weak transcription	NH-A	brain
18	chr15:31325800-31327000	Enhancers	Primary B cells from peripheral blood	blood
19	chr15:31325800-31328800	Weak transcription	HSMMtube	muscle
20	chr15:31326000-31332200	Weak transcription	Spleen	Spleen
21	chr15:31326200-31326800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr15:31326200-31326800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr15:31326200-31327800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:31326400-31328200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:31326400-31328400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:31326600-31326800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:31326600-31326800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr15:31326600-31329600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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