Variant report

Variant	rs28716534
Chromosome Location	chr5:17217206-17217207
allele	A/T
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	E2F6	chr5:17215660-17217396	A549	lung:	n/a	chr5:17216123-17216132 chr5:17216400-17216408 chr5:17217250-17217259 chr5:17217247-17217257
2	RAD21	chr5:17216041-17217409	IMR90	lung:	n/a	n/a
3	MAX	chr5:17216155-17217462	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr5:17216102-17217290	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr5:17217141-17217251	Kidney_OC	kidney:	n/a	n/a
6	CTBP2	chr5:17216156-17217263	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr5:17216131-17217425	H1-hESC	embryonic stem cell:	n/a	n/a
8	NFIC	chr5:17216148-17217326	ECC-1	luminal epithelium:	n/a	n/a
9	GATA3	chr5:17216950-17217998	A549	lung:	n/a	n/a
10	BRCA1	chr5:17215786-17217331	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr5:17217181-17217293	A549	lung:	n/a	n/a
12	MAX	chr5:17216185-17217215	H1-hESC	embryonic stem cell:	n/a	n/a
13	SMARCC2	chr5:17216014-17217258	Hela-S3	cervix:	n/a	n/a
14	FOXA2	chr5:17217043-17217488	A549	lung:	n/a	n/a
15	NR3C1	chr5:17216928-17217404	A549	lung:	n/a	n/a
16	HDAC2	chr5:17216043-17217490	MCF-7	breast:	n/a	chr5:17216098-17216107
17	RCOR1	chr5:17216146-17217216	GM12878	blood:	n/a	n/a
18	CHD2	chr5:17216100-17219472	Hela-S3	cervix:	n/a	chr5:17218841-17218851 chr5:17218352-17218362 chr5:17218195-17218205
19	RAD21	chr5:17215696-17217908	SK-N-SH	brain:	n/a	chr5:17217826-17217839
20	TCF12	chr5:17217023-17217428	A549	lung:	n/a	n/a
21	GATA3	chr5:17216024-17218174	A549	lung:	n/a	chr5:17218110-17218119
22	CHD2	chr5:17216253-17217409	GM12878	blood:	n/a	n/a
23	SP1	chr5:17215936-17217943	A549	lung:	n/a	chr5:17217486-17217500
24	POLR2A	chr5:17216454-17217331	HL-60	blood:	n/a	n/a
25	SIN3AK20	chr5:17216688-17217220	PANC-1	pancreas:	n/a	n/a
26	EP300	chr5:17215962-17217908	A549	lung:	n/a	n/a
27	JUND	chr5:17216189-17217331	H1-hESC	embryonic stem cell:	n/a	n/a
28	ZZZ3	chr5:17217012-17217348	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr5:17215899-17217427	SK-N-SH	brain:	n/a	n/a
30	YY1	chr5:17217059-17217563	ECC-1	luminal epithelium:	n/a	chr5:17217250-17217259 chr5:17217250-17217264 chr5:17217247-17217261
31	MAX	chr5:17215806-17219739	A549	lung:	n/a	chr5:17218380-17218390
32	SMC3	chr5:17216129-17217268	GM12878	blood:	n/a	chr5:17217247-17217257
33	YY1	chr5:17216251-17217875	ECC-1	luminal epithelium:	n/a	chr5:17217821-17217835 chr5:17217250-17217259 chr5:17217250-17217264 chr5:17217247-17217261
34	ZBTB7A	chr5:17216387-17217866	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr5:17216169-17217240	GM12878	blood:	n/a	n/a
36	CTCF	chr5:17217180-17217330	GM12878	blood:	n/a	n/a
37	TCF7L2	chr5:17216093-17217341	Hela-S3	cervix:	n/a	n/a
38	MAX	chr5:17216069-17217307	Hela-S3	cervix:	n/a	n/a
39	CHD2	chr5:17216229-17217302	H1-hESC	embryonic stem cell:	n/a	n/a
40	BCL3	chr5:17215965-17217474	A549	lung:	n/a	chr5:17217253-17217262 chr5:17217256-17217265 chr5:17217251-17217264
41	CTCF	chr5:17217096-17217280	ProgFib	skin:	n/a	n/a
42	POLR2A	chr5:17216113-17217375	PANC-1	pancreas:	n/a	n/a
43	E2F6	chr5:17215742-17217278	H1-hESC	embryonic stem cell:	n/a	chr5:17216123-17216132 chr5:17216400-17216408 chr5:17217250-17217259 chr5:17217247-17217257
44	ELK1	chr5:17216077-17217289	Hela-S3	cervix:	n/a	n/a
45	RAD21	chr5:17215985-17217405	A549	lung:	n/a	n/a
46	MTA3	chr5:17216156-17217419	GM12878	blood:	n/a	n/a
47	MAX	chr5:17216133-17217399	ECC-1	luminal epithelium:	n/a	n/a
48	MAFK	chr5:17215610-17217327	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:17217161-17217406	A549	lung:	n/a	n/a
50	EP300	chr5:17216005-17218133	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:17215544..17223113-chr5:17298591..17308160,18	MCF-7	breast:
2	chr5:17216395..17218536-chr5:17655025..17657774,2	MCF-7	breast:
3	chr5:17215446..17220855-chr5:17303141..17309835,13	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYO10-1	chr5:17216508-17217508	ENSG00000215196
2	lnc-MYO10-1	chr5:17216186-17217531	NONHSAT100620

Variant related genes	Relation type
BASP1	TF binding region
ENSG00000215196	TF binding region
ENSG00000269466	Chromatin interaction
ENSG00000185296	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv830218	chr5:17093162-17290045	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv4738	chr5:17178267-17223677	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv521697	chr5:17211649-17225333	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv597312	chr5:17214901-17225333	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv823015	chr5:17216009-17219199	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
9	esv3343514	chr5:17216052-17219850	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
10	esv3409498	chr5:17216377-17219325	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
11	esv3340625	chr5:17216602-17219300	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
12	esv3420964	chr5:17217002-17219850	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17213600-17222200	Active TSS	Fetal Brain Female	brain
2	chr5:17214000-17219800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:17214600-17219400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr5:17214800-17218800	Active TSS	A549	lung
5	chr5:17215000-17219400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr5:17215400-17219800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr5:17215400-17221000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:17215600-17217400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr5:17215600-17219000	Active TSS	Brain Cingulate Gyrus	brain
10	chr5:17215800-17219400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr5:17215800-17219400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:17215800-17220400	Active TSS	Brain Anterior Caudate	brain
13	chr5:17216000-17219400	Active TSS	Fetal Kidney	kidney
14	chr5:17216200-17219200	Active TSS	NHLF	lung
15	chr5:17216200-17219400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr5:17216200-17219400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:17216200-17219800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr5:17216200-17219800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:17216400-17217400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr5:17216400-17217400	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr5:17216400-17217400	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr5:17216400-17217400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr5:17216400-17217400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr5:17216400-17217400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:17216400-17217400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:17216400-17217400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr5:17216400-17217400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
28	chr5:17216400-17217400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr5:17216400-17217400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
30	chr5:17216400-17217400	Flanking Active TSS	Placenta	Placenta
31	chr5:17216400-17217400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr5:17216400-17218400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr5:17216400-17218600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:17216400-17219000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
35	chr5:17216400-17219200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:17216400-17219200	Active TSS	Aorta	Aorta
37	chr5:17216400-17219200	Active TSS	Brain Substantia Nigra	brain
38	chr5:17216400-17219200	Active TSS	Osteobl	bone
39	chr5:17216400-17219400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:17216400-17219400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr5:17216400-17219400	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr5:17216400-17219400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr5:17216400-17219400	Active TSS	HSMM	muscle
44	chr5:17216400-17219600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:17216400-17219600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:17216400-17219600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:17216400-17219600	Active TSS	Ovary	ovary
48	chr5:17216400-17219600	Active TSS	Rectal Smooth Muscle	rectum
49	chr5:17216400-17219800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr5:17216400-17219800	Active TSS	HSMMtube	muscle

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