Variant report

Variant	rs12708517
Chromosome Location	chr15:75508970-75508971
allele	A/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	ELF1	chr15:75505530-75509026	GM12878	blood:	n/a	chr15:75505566-75505578
2	POLR2A	chr15:75505475-75509060	U87	brain:	n/a	n/a
3	POLR2A	chr15:75506292-75509098	U87	brain:	n/a	n/a
4	POLR2A	chr15:75504559-75509010	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr15:75499212-75509025	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:75499180-75510106	GM12892	blood:	n/a	n/a
7	NFATC1	chr15:75504997-75509017	GM12878	blood:	n/a	n/a
8	BCL3	chr15:75508620-75508997	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75503181-75509014	GM12892	blood:	n/a	n/a
10	POLR2A	chr15:75507334-75509020	ECC-1	luminal epithelium:	n/a	n/a
11	STAT5A	chr15:75508263-75509030	GM12878	blood:	n/a	chr15:75508442-75508454
12	POLR2A	chr15:75503737-75510069	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:75504821-75509048	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr15:75499185-75510301	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:75499197-75508973	GM12878	blood:	n/a	n/a
16	MTA3	chr15:75504571-75509033	GM12878	blood:	n/a	n/a
17	TCF3	chr15:75508547-75508975	GM12878	blood:	n/a	chr15:75508774-75508788
18	POLR2A	chr15:75499231-75510144	GM12891	blood:	n/a	n/a
19	POLR2A	chr15:75499943-75509044	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:75499660-75510103	GM12891	blood:	n/a	n/a
21	POLR2A	chr15:75498005-75509029	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:75499226-75510058	GM12892	blood:	n/a	n/a
23	POLR2A	chr15:75489631-75513671	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000261779	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11072532	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11072533	0.94[ASN][1000 genomes]
rs11072534	0.90[ASN][1000 genomes]
rs11853027	0.90[ASN][1000 genomes]
rs12591506	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1532155	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3743210	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3743211	0.89[ASN][1000 genomes]
rs4886431	0.86[ASN][1000 genomes]
rs4886677	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7403344	0.94[ASN][1000 genomes]
rs8025431	0.89[ASN][1000 genomes]
rs8039284	0.89[ASN][1000 genomes]
rs8043432	0.90[ASN][1000 genomes]
rs902482	0.89[ASN][1000 genomes]
rs953555	0.90[ASN][1000 genomes]

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	nsv904383	chr15:75382542-75520378	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1796196	chr15:75389382-75531124	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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	96 gene(s)	inside rSNPs	diseases
4	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv1053212	chr15:75428467-75534408	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv833056	chr15:75452947-75614590	Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv904384	chr15:75493823-75520378	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv569995	chr15:75493823-75537475	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv569996	chr15:75493823-75540491	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv904385	chr15:75493823-75546700	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS 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 target site	42 gene(s)	inside rSNPs	diseases
11	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
12	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75500000-75510200	Strong transcription	Fetal Intestine Small	intestine
2	chr15:75504200-75511400	Weak transcription	Stomach Mucosa	stomach
3	chr15:75504800-75515800	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:75505600-75509000	Weak transcription	HSMMtube	muscle
5	chr15:75505600-75511400	Weak transcription	Liver	Liver
6	chr15:75505800-75509000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:75505800-75510400	Weak transcription	GM12878-XiMat	blood
8	chr15:75505800-75511000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:75505800-75511200	Weak transcription	Colonic Mucosa	Colon
10	chr15:75505800-75511400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr15:75505800-75511600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:75505800-75512200	Weak transcription	Aorta	Aorta
13	chr15:75505800-75521400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:75506000-75509600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:75506000-75511000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:75506000-75511000	Weak transcription	HepG2	liver
17	chr15:75506000-75513800	Weak transcription	Pancreas	Pancrea
18	chr15:75506200-75509600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr15:75506200-75512000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:75506400-75509000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:75506400-75509800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:75506400-75511200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:75506400-75511800	Weak transcription	Left Ventricle	heart
24	chr15:75506600-75512000	Weak transcription	Primary B cells from cord blood	blood
25	chr15:75506600-75512200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:75506600-75514600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:75506800-75510600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr15:75506800-75510800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:75506800-75511200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:75506800-75514800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:75506800-75518400	Weak transcription	Ovary	ovary
32	chr15:75507000-75509000	Weak transcription	Dnd41	blood
33	chr15:75507000-75509800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:75507000-75509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:75507000-75510000	Weak transcription	Fetal Intestine Large	intestine
36	chr15:75507000-75510200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:75507000-75511200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr15:75507000-75516800	Weak transcription	Gastric	stomach
39	chr15:75507200-75509000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:75507200-75509600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:75507200-75509600	Weak transcription	Adipose Nuclei	Adipose
42	chr15:75507400-75517000	Weak transcription	Esophagus	oesophagus
43	chr15:75507400-75518200	Weak transcription	Lung	lung
44	chr15:75507600-75509600	Enhancers	Placenta	Placenta
45	chr15:75507600-75512600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:75507800-75509000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:75507800-75512200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr15:75508000-75512600	Weak transcription	Fetal Stomach	stomach
49	chr15:75508000-75517400	Weak transcription	Right Ventricle	heart
50	chr15:75508200-75509000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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