Variant report

Variant	rs541108055
Chromosome Location	chr5:17216994-17216995
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	POLR2A	chr5:17216775-17217141	A549	lung:	n/a	n/a
2	E2F6	chr5:17215660-17217396	A549	lung:	n/a	chr5:17216123-17216132 chr5:17216400-17216408 chr5:17217250-17217259 chr5:17217247-17217257
3	RAD21	chr5:17216041-17217409	IMR90	lung:	n/a	n/a
4	MAX	chr5:17216158-17217126	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr5:17216155-17217462	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZNF143	chr5:17216102-17217290	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3AK20	chr5:17216779-17217184	A549	lung:	n/a	n/a
8	CTBP2	chr5:17216156-17217263	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr5:17216131-17217425	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr5:17216510-17217072	GM12891	blood:	n/a	n/a
11	TCF12	chr5:17216691-17217015	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr5:17216298-17217088	H1-hESC	embryonic stem cell:	n/a	n/a
13	NFIC	chr5:17216148-17217326	ECC-1	luminal epithelium:	n/a	n/a
14	GATA3	chr5:17216950-17217998	A549	lung:	n/a	n/a
15	BRCA1	chr5:17215786-17217331	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr5:17216126-17217194	H1-hESC	embryonic stem cell:	n/a	n/a
17	CHD1	chr5:17216903-17217103	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr5:17216212-17216994	SK-N-SH	brain:	n/a	n/a
19	MAX	chr5:17216185-17217215	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr5:17216960-17217110	NHDF-neo	bronchial:	n/a	n/a
21	SMARCC2	chr5:17216014-17217258	Hela-S3	cervix:	n/a	n/a
22	YY1	chr5:17216182-17217047	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:17216892-17216995	MCF-7	breast:	n/a	n/a
24	POLR2A	chr5:17216529-17217172	A549	lung:	n/a	n/a
25	NR3C1	chr5:17216928-17217404	A549	lung:	n/a	n/a
26	HDAC2	chr5:17216043-17217490	MCF-7	breast:	n/a	chr5:17216098-17216107
27	RCOR1	chr5:17216146-17217216	GM12878	blood:	n/a	n/a
28	NRF1	chr5:17216873-17217034	GM12878	blood:	n/a	n/a
29	CHD2	chr5:17216100-17219472	Hela-S3	cervix:	n/a	chr5:17218841-17218851 chr5:17218352-17218362 chr5:17218195-17218205
30	REST	chr5:17216885-17217193	A549	lung:	n/a	n/a
31	RAD21	chr5:17215696-17217908	SK-N-SH	brain:	n/a	chr5:17217826-17217839
32	GATA3	chr5:17216024-17218174	A549	lung:	n/a	chr5:17218110-17218119
33	CHD2	chr5:17216253-17217409	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:17216668-17217051	A549	lung:	n/a	n/a
35	SP1	chr5:17215936-17217943	A549	lung:	n/a	chr5:17217486-17217500
36	POLR2A	chr5:17216454-17217331	HL-60	blood:	n/a	n/a
37	SIN3AK20	chr5:17216688-17217220	PANC-1	pancreas:	n/a	n/a
38	EP300	chr5:17215962-17217908	A549	lung:	n/a	n/a
39	JUND	chr5:17216189-17217331	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr5:17216142-17217056	SK-N-SH_RA	brain:	n/a	n/a
41	CTCF	chr5:17215899-17217427	SK-N-SH	brain:	n/a	n/a
42	MAX	chr5:17215806-17219739	A549	lung:	n/a	chr5:17218380-17218390
43	MYC	chr5:17216981-17217135	H1-hESC	embryonic stem cell:	n/a	n/a
44	SMC3	chr5:17216129-17217268	GM12878	blood:	n/a	chr5:17217247-17217257
45	YY1	chr5:17216251-17217875	ECC-1	luminal epithelium:	n/a	chr5:17217821-17217835 chr5:17217250-17217259 chr5:17217250-17217264 chr5:17217247-17217261
46	ZBTB7A	chr5:17216387-17217866	ECC-1	luminal epithelium:	n/a	n/a
47	CTCF	chr5:17216169-17217240	GM12878	blood:	n/a	n/a
48	TCF7L2	chr5:17216093-17217341	Hela-S3	cervix:	n/a	n/a
49	MAX	chr5:17216069-17217307	Hela-S3	cervix:	n/a	n/a
50	CHD2	chr5:17216229-17217302	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:17215544..17223113-chr5:17298591..17308160,18	MCF-7	breast:
2	chr5:17215630..17217000-chr5:18305120..18306424,11	MCF-7	breast:
3	chr5:17216395..17218536-chr5:17655025..17657774,2	MCF-7	breast:
4	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	chr5:17216186-17217156	ENSG00000215196
3	lnc-MYO10-1	chr5:17216186-17217531	NONHSAT100620

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

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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	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

No data

Chromatin state (count:115 , 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	chr5:17213800-17217200	Active TSS	Fetal Brain Male	brain
3	chr5:17214000-17219800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:17214600-17219400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:17214800-17218800	Active TSS	A549	lung
6	chr5:17215000-17217200	Flanking Active TSS	Hela-S3	cervix
7	chr5:17215000-17219400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:17215200-17217200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr5:17215400-17219800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr5:17215400-17221000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:17215600-17217400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr5:17215600-17219000	Active TSS	Brain Cingulate Gyrus	brain
13	chr5:17215800-17219400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr5:17215800-17219400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:17215800-17220400	Active TSS	Brain Anterior Caudate	brain
16	chr5:17216000-17217200	Enhancers	Liver	Liver
17	chr5:17216000-17219400	Active TSS	Fetal Kidney	kidney
18	chr5:17216200-17217000	Flanking Active TSS	NH-A	brain
19	chr5:17216200-17217200	Enhancers	Pancreas	Pancrea
20	chr5:17216200-17219200	Active TSS	NHLF	lung
21	chr5:17216200-17219400	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr5:17216200-17219400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:17216200-17219800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr5:17216200-17219800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:17216400-17217000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr5:17216400-17217000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:17216400-17217000	ZNF genes & repeats	Right Atrium	heart
28	chr5:17216400-17217000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
29	chr5:17216400-17217000	Flanking Active TSS	HMEC	breast
30	chr5:17216400-17217000	Flanking Active TSS	NHEK	skin
31	chr5:17216400-17217200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr5:17216400-17217200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:17216400-17217200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:17216400-17217200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr5:17216400-17217200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
36	chr5:17216400-17217200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr5:17216400-17217200	Flanking Active TSS	Fetal Stomach	stomach
38	chr5:17216400-17217200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
39	chr5:17216400-17217200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
40	chr5:17216400-17217200	Flanking Active TSS	HUVEC	blood vessel
41	chr5:17216400-17217400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr5:17216400-17217400	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr5:17216400-17217400	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr5:17216400-17217400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr5:17216400-17217400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr5:17216400-17217400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:17216400-17217400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:17216400-17217400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr5:17216400-17217400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
50	chr5:17216400-17217400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland

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