Variant report

Variant	rs28517433
Chromosome Location	chr15:62353292-62353293
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	EP300	chr15:62353239-62353418	GM12878	blood:	n/a	chr15:62353388-62353402
2	TCF7L2	chr15:62351997-62353327	Hela-S3	cervix:	n/a	n/a
3	TCF7L2	chr15:62352077-62353360	PANC-1	pancreas:	n/a	n/a
4	CHD2	chr15:62351850-62353366	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:62351914-62353381	GM19193	blood:	n/a	n/a
6	WRNIP1	chr15:62351824-62353304	GM12878	blood:	n/a	n/a
7	CTCF	chr15:62353220-62353370	HMEC	breast:	n/a	n/a
8	POLR2A	chr15:62353201-62353339	MCF10A-Er-Src	breast:	n/a	n/a
9	MAX	chr15:62351849-62353320	HCT-116	colon:	n/a	n/a
10	MXI1	chr15:62351331-62353306	IMR90	lung:	n/a	chr15:62353005-62353020
11	NFIC	chr15:62351788-62353409	GM12878	blood:	n/a	n/a
12	RCOR1	chr15:62351813-62353472	IMR90	lung:	n/a	n/a
13	CTCF	chr15:62353240-62353390	NHDF-neo	bronchial:	n/a	n/a
14	GATA1	chr15:62351266-62353595	PBDE	blood:	n/a	n/a
15	HA-E2F1	chr15:62352022-62353360	MCF-7	breast:	n/a	chr15:62352705-62352714 chr15:62352929-62352936 chr15:62352928-62352940 chr15:62352929-62352936 chr15:62352929-62352936
16	SMARCC1	chr15:62351874-62353299	Hela-S3	cervix:	n/a	n/a
17	MAZ	chr15:62351374-62353310	IMR90	lung:	n/a	n/a
18	POLR2A	chr15:62351741-62353450	PBDE	blood:	n/a	n/a
19	E2F6	chr15:62351875-62353312	A549	lung:	n/a	chr15:62352705-62352714 chr15:62352929-62352936 chr15:62352928-62352940 chr15:62352929-62352936 chr15:62352929-62352936
20	E2F4	chr15:62352536-62353352	MCF10A-Er-Src	breast:	n/a	chr15:62352705-62352714 chr15:62352929-62352936 chr15:62352928-62352940 chr15:62352929-62352936 chr15:62352929-62352936
21	RAD21	chr15:62351155-62353498	SK-N-SH	brain:	n/a	chr15:62352443-62352455 chr15:62352416-62352429 chr15:62352621-62352634
22	BHLHE40	chr15:62351886-62353472	GM12878	blood:	n/a	chr15:62352932-62352948 chr15:62352966-62352982
23	EBF1	chr15:62353271-62353418	GM12878	blood:	n/a	n/a
24	MAZ	chr15:62351726-62353333	GM12878	blood:	n/a	n/a
25	EP300	chr15:62351860-62353444	GM12878	blood:	n/a	chr15:62352044-62352053 chr15:62353388-62353402
26	MAZ	chr15:62351760-62353395	K562	blood:	n/a	n/a
27	CTCF	chr15:62353200-62353350	HPF	lung:	n/a	n/a
28	CTCF	chr15:62351357-62353929	A549	lung:	n/a	chr15:62352934-62352952 chr15:62352941-62352949
29	RUNX3	chr15:62351877-62353496	GM12878	blood:	n/a	n/a
30	SMARCB1	chr15:62351966-62353308	Hela-S3	cervix:	n/a	n/a
31	MAX	chr15:62351865-62353380	ECC-1	luminal epithelium:	n/a	n/a
32	MAX	chr15:62351706-62353453	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:62351577-62353420	Raji	blood:	n/a	n/a
34	E2F6	chr15:62351896-62353336	H1-hESC	embryonic stem cell:	n/a	chr15:62352705-62352714 chr15:62352929-62352936 chr15:62352928-62352940 chr15:62352929-62352936 chr15:62352929-62352936
35	RUNX3	chr15:62351832-62353572	GM12878	blood:	n/a	n/a
36	MXI1	chr15:62351352-62353444	SK-N-SH	brain:	n/a	chr15:62353005-62353020
37	HCFC1	chr15:62351216-62354024	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62352901..62356622-chr15:62357854..62362137,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2CD4A-1	chr15:62353167-62353462	XLOC_011278
2	lnc-C2CD4A-1	chr15:62352713-62354633	ENSG00000259251.2
3	lnc-C2CD4A-1	chr15:62353167-62353473	ENSG00000259251.2

Variant related genes	Relation type
VPS13C	TF binding region
ENSG00000198535	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13329329	0.90[ASN][1000 genomes]
rs13329639	0.90[ASN][1000 genomes]
rs17238301	0.93[ASN][1000 genomes]
rs28367150	0.90[ASN][1000 genomes]
rs28403096	0.81[ASN][1000 genomes]
rs28408506	0.90[ASN][1000 genomes]
rs28411845	0.86[ASN][1000 genomes]
rs28493143	0.90[ASN][1000 genomes]
rs28541511	0.90[ASN][1000 genomes]
rs28583709	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28613580	0.90[ASN][1000 genomes]
rs28650099	0.90[ASN][1000 genomes]
rs28654580	0.86[ASN][1000 genomes]
rs28664955	0.90[ASN][1000 genomes]
rs28692770	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28708564	0.86[ASN][1000 genomes]
rs28720854	0.84[ASN][1000 genomes]
rs28721460	0.86[ASN][1000 genomes]
rs28758709	0.86[ASN][1000 genomes]
rs28783433	0.90[ASN][1000 genomes]
rs28810829	0.86[ASN][1000 genomes]
rs3784631	0.81[ASN][1000 genomes]
rs57422239	0.96[ASN][1000 genomes]
rs725174	0.90[ASN][1000 genomes]
rs73414700	0.90[ASN][1000 genomes]
rs73416527	0.90[ASN][1000 genomes]
rs73416547	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027343	0.90[ASN][1000 genomes]
rs8042267	0.81[ASN][1000 genomes]
rs9920015	0.90[ASN][1000 genomes]
rs9920581	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62350800-62353600	Active TSS	NHDF-Ad	bronchial
2	chr15:62351000-62353600	Active TSS	Right Atrium	heart
3	chr15:62351000-62353800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:62351200-62353400	Active TSS	NHLF	lung
5	chr15:62351200-62353800	Active TSS	GM12878-XiMat	blood
6	chr15:62351400-62353400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:62351400-62353400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr15:62351400-62353400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:62351400-62353400	Active TSS	Colonic Mucosa	Colon
10	chr15:62351400-62353400	Active TSS	Fetal Brain Female	brain
11	chr15:62351400-62353400	Active TSS	Psoas Muscle	Psoas
12	chr15:62351400-62353400	Active TSS	A549	lung
13	chr15:62351400-62353600	Active TSS	Aorta	Aorta
14	chr15:62351400-62353600	Active TSS	Fetal Brain Male	brain
15	chr15:62351400-62353600	Active TSS	HSMMtube	muscle
16	chr15:62351400-62353800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:62351400-62354000	Active TSS	Primary T cells fromperipheralblood	blood
18	chr15:62351600-62353400	Active TSS	Fetal Kidney	kidney
19	chr15:62351600-62353400	Active TSS	Right Ventricle	heart
20	chr15:62351600-62353400	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr15:62351600-62353400	Active TSS	Small Intestine	intestine
22	chr15:62351600-62353400	Active TSS	Stomach Mucosa	stomach
23	chr15:62351600-62353600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr15:62351600-62353600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:62351600-62353600	Active TSS	Brain Cingulate Gyrus	brain
26	chr15:62351600-62353600	Active TSS	Brain Hippocampus Middle	brain
27	chr15:62351600-62353600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:62351600-62353600	Active TSS	Colon Smooth Muscle	Colon
29	chr15:62351600-62353600	Active TSS	Fetal Thymus	thymus
30	chr15:62351600-62353800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:62351600-62353800	Active TSS	Brain Substantia Nigra	brain
32	chr15:62351600-62353800	Active TSS	Ovary	ovary
33	chr15:62351600-62354600	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr15:62351800-62353400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr15:62351800-62353400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:62351800-62353400	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr15:62351800-62353400	Active TSS	Esophagus	oesophagus
38	chr15:62351800-62353400	Active TSS	Fetal Lung	lung
39	chr15:62351800-62353400	Active TSS	Gastric	stomach
40	chr15:62351800-62353400	Active TSS	Left Ventricle	heart
41	chr15:62351800-62353400	Active TSS	Lung	lung
42	chr15:62351800-62353400	Active TSS	Dnd41	blood
43	chr15:62351800-62353600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:62351800-62353600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:62351800-62353600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr15:62351800-62353600	Active TSS	Rectal Smooth Muscle	rectum
47	chr15:62351800-62353600	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr15:62351800-62353800	Active TSS	Brain Anterior Caudate	brain
49	chr15:62351800-62353800	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr15:62351800-62353800	Active TSS	Rectal Mucosa Donor 29	rectum

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