Variant report

Variant	rs12915819
Chromosome Location	chr15:99856091-99856092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr15:99855847-99856338	ECC-1	luminal epithelium:	n/a	n/a
2	FOS	chr15:99855981-99856136	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr15:99855781-99856133	MCF-7	breast:	n/a	n/a
4	STAT3	chr15:99855902-99856178	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr15:99855780-99856160	HCT-116	colon:	n/a	n/a
6	JUND	chr15:99855967-99856207	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr15:99855692-99856283	SK-N-SH	brain:	n/a	n/a
8	CBX3	chr15:99855814-99856323	HCT-116	colon:	n/a	n/a
9	FOS	chr15:99855923-99856168	MCF10A-Er-Src	breast:	n/a	n/a
10	TEAD4	chr15:99855894-99856141	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOS	chr15:99855907-99856197	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr15:99855921-99856156	MCF10A-Er-Src	breast:	n/a	n/a
13	TCF12	chr15:99855666-99856360	SK-N-SH	brain:	n/a	n/a
14	STAT3	chr15:99855912-99856204	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr15:99855854-99856147	MCF10A-Er-Src	breast:	n/a	n/a
16	TEAD4	chr15:99855943-99856157	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr15:99855887-99856297	HCT-116	colon:	n/a	n/a
18	TEAD4	chr15:99855870-99856201	HCT-116	colon:	n/a	n/a
19	JUND	chr15:99855773-99856351	HCT-116	colon:	n/a	n/a
20	FOS	chr15:99855920-99856135	MCF10A-Er-Src	breast:	n/a	n/a
21	EP300	chr15:99855703-99856432	ECC-1	luminal epithelium:	n/a	n/a
22	STAT3	chr15:99855903-99856183	MCF10A-Er-Src	breast:	n/a	n/a
23	TEAD4	chr15:99855861-99856268	ECC-1	luminal epithelium:	n/a	n/a
24	FOSL1	chr15:99855785-99856382	HCT-116	colon:	n/a	n/a
25	TCF12	chr15:99855646-99856353	ECC-1	luminal epithelium:	n/a	n/a
26	NFIC	chr15:99855780-99856269	ECC-1	luminal epithelium:	n/a	n/a
27	TEAD4	chr15:99855844-99856282	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99846877..99849995-chr15:99854925..99857345,3	MCF-7	breast:

No data

Variant related genes	Relation type
LRRC28	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10152912	0.91[ASN][1000 genomes]
rs1223950	0.88[ASN][1000 genomes]
rs1223951	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12437806	0.87[ASN][1000 genomes]
rs12907394	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12911768	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567416	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976589	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1976590	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2048301	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602030	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2862139	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3937681	0.84[EUR][1000 genomes]
rs4344722	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4965224	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6598231	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7164003	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042021	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9920418	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
18	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
20	nsv516288	chr15:99855009-99856849	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99793000-99866600	Weak transcription	Gastric	stomach
2	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
3	chr15:99835200-99864200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:99847400-99877200	Weak transcription	Ovary	ovary
5	chr15:99848200-99860800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:99848400-99860600	Weak transcription	HepG2	liver
7	chr15:99848400-99860800	Weak transcription	NH-A	brain
8	chr15:99850400-99863800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:99853000-99876000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:99853200-99875400	Weak transcription	Fetal Thymus	thymus
11	chr15:99853600-99875800	Weak transcription	Fetal Intestine Large	intestine
12	chr15:99854200-99860600	Weak transcription	Liver	Liver
13	chr15:99854200-99864200	Weak transcription	Left Ventricle	heart
14	chr15:99854400-99860600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:99854400-99863600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:99854400-99864000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:99854400-99876000	Weak transcription	Dnd41	blood
18	chr15:99855600-99856200	Enhancers	NHEK	skin
19	chr15:99855800-99856200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:99855800-99856200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:99856000-99856200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:99856000-99856200	Enhancers	HMEC	breast
23	chr15:99856000-99856200	Enhancers	HUVEC	blood vessel
24	chr15:99856000-99857200	Enhancers	A549	lung

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