Variant report

Variant	rs546653062
Chromosome Location	chr5:92919538-92919539
allele	C/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	TCF7L2	chr5:92919490-92919840	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:92919377-92919879	H1-neurons	neurons:	n/a	n/a
3	SIN3AK20	chr5:92919461-92920475	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr5:92919425-92922226	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr5:92917513-92922404	SK-N-SH	brain:	n/a	chr5:92918848-92918863
6	POLR2A	chr5:92918370-92920285	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:92918008-92919908	H1-neurons	neurons:	n/a	n/a
8	MYC	chr5:92919383-92919572	MCF10A-Er-Src	breast:	n/a	n/a
9	CHD1	chr5:92919424-92920196	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTBP2	chr5:92919429-92921750	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:92919533-92919888	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr5:92919472-92920408	Hela-S3	cervix:	n/a	n/a
13	TCF12	chr5:92915441-92919825	A549	lung:	n/a	chr5:92918800-92918810
14	POLR2A	chr5:92919528-92920315	Hela-S3	cervix:	n/a	n/a
15	MAZ	chr5:92919538-92921594	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr5:92918085-92919590	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr5:92919519-92920583	HUVEC	blood vessel:	n/a	n/a
18	MAZ	chr5:92918142-92920671	IMR90	lung:	n/a	chr5:92918679-92918689 chr5:92918682-92918692 chr5:92918653-92918663 chr5:92918596-92918606
19	POLR2A	chr5:92918245-92920378	MCF10A-Er-Src	breast:	n/a	n/a
20	RAD21	chr5:92918280-92920333	IMR90	lung:	n/a	n/a
21	POLR2A	chr5:92917672-92920232	IMR90	lung:	n/a	n/a
22	POLR2A	chr5:92918332-92922151	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr5:92919534-92919582	HepG2	liver:	n/a	n/a
24	CHD1	chr5:92912776-92927520	IMR90	lung:	n/a	chr5:92914877-92914887 chr5:92926304-92926314 chr5:92917311-92917321 chr5:92918655-92918665 chr5:92918684-92918694 chr5:92920697-92920707 chr5:92920384-92920394 chr5:92915468-92915478 chr5:92917327-92917337 chr5:92920376-92920386
25	POLR2A	chr5:92919524-92919815	Hela-S3	cervix:	n/a	n/a
26	ZNF263	chr5:92915496-92920299	HEK293-T-REx	kidney:	n/a	chr5:92920015-92920024 chr5:92917326-92917335 chr5:92918616-92918625 chr5:92917212-92917221
27	POLR2A	chr5:92918315-92919734	HUVEC	blood vessel:	n/a	n/a
28	HEY1	chr5:92919477-92920360	HepG2	liver:	n/a	chr5:92919632-92919647
29	TCF7L2	chr5:92919527-92920338	HCT-116	colon:	n/a	n/a
30	SMC3	chr5:92914300-92920526	SK-N-SH	brain:	n/a	chr5:92915792-92915800 chr5:92915472-92915482 chr5:92917256-92917270
31	TCF7L2	chr5:92919524-92919803	MCF-7	breast:	n/a	n/a
32	POLR2A	chr5:92919423-92920347	HUVEC	blood vessel:	n/a	n/a
33	REST	chr5:92919537-92919818	HepG2	liver:	n/a	chr5:92919794-92919807
34	SIN3A	chr5:92919513-92920030	H1-hESC	embryonic stem cell:	n/a	chr5:92919858-92919871 chr5:92919702-92919713 chr5:92919794-92919807
35	MXI1	chr5:92919483-92920525	IMR90	lung:	n/a	n/a
36	TCF7L2	chr5:92918322-92919658	HEK293	kidney:	n/a	n/a
37	MAX	chr5:92919425-92920411	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:92919342..92920132-chr9:33025119..33025739,2	HCT-116	colon:
2	chr5:92914959..92917781-chr5:92918156..92922060,3	MCF-7	breast:
3	chr5:92918392..92920422-chr5:92954459..92956574,2	MCF-7	breast:

Variant related genes	Relation type
NR2F1	TF binding region
NR2F1-AS1	TF binding region
ENSG00000137074	Chromatin interaction
ENSG00000086061	Chromatin interaction
ENSG00000237187	Chromatin interaction
ENSG00000251725	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451945	chr5:92858750-93024740	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv830404	chr5:92868336-93048257	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv1819334	chr5:92892591-92956733	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv882383	chr5:92895401-92928346	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv823130	chr5:92896346-92966016	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv4918	chr5:92898426-92943359	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv823132	chr5:92898512-92969668	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv3423958	chr5:92919096-92921969	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
9	esv3468495	chr5:92919221-92922169	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
10	esv3468497	chr5:92919221-92922169	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92913800-92923200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:92914000-92919800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
3	chr5:92914000-92919800	Active TSS	Fetal Kidney	kidney
4	chr5:92914000-92925800	Active TSS	Brain Angular Gyrus	brain
5	chr5:92914200-92919800	Bivalent/Poised TSS	Fetal Stomach	stomach
6	chr5:92914200-92921600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:92914200-92926200	Active TSS	Fetal Brain Female	brain
8	chr5:92914400-92922200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:92914400-92922800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:92914600-92919800	Active TSS	NHDF-Ad	bronchial
11	chr5:92914600-92924600	Active TSS	HSMM	muscle
12	chr5:92914600-92924800	Active TSS	Right Atrium	heart
13	chr5:92914800-92920800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:92914800-92921800	Active TSS	Psoas Muscle	Psoas
15	chr5:92914800-92921800	Active TSS	Osteobl	bone
16	chr5:92914800-92923200	Active TSS	Ovary	ovary
17	chr5:92914800-92926000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:92915000-92921600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr5:92915000-92922200	Active TSS	HSMMtube	muscle
20	chr5:92915200-92921000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:92915200-92921000	Active TSS	NHLF	lung
22	chr5:92915200-92921600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:92915200-92923200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:92915200-92923600	Active TSS	NH-A	brain
25	chr5:92916200-92921600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:92916200-92927600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr5:92916400-92923200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr5:92916400-92923400	Active TSS	Stomach Smooth Muscle	stomach
29	chr5:92916400-92925200	Active TSS	Brain Substantia Nigra	brain
30	chr5:92916800-92919800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr5:92916800-92921600	Active TSS	Brain Cingulate Gyrus	brain
32	chr5:92917000-92919800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:92917000-92920800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:92917000-92921000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr5:92917000-92921400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:92917200-92919600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
37	chr5:92917200-92919600	Weak transcription	Spleen	Spleen
38	chr5:92917200-92919800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
39	chr5:92917200-92919800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:92917200-92920000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
41	chr5:92917200-92921000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr5:92917600-92919600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr5:92917800-92919800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr5:92918000-92921600	Bivalent/Poised TSS	NHEK	skin
45	chr5:92918000-92925000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:92918200-92919800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr5:92918400-92919600	Active TSS	Pancreas	Pancrea
48	chr5:92918400-92919600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
49	chr5:92918400-92919600	Bivalent Enhancer	Dnd41	blood
50	chr5:92918400-92919800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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