Variant report

Variant	rs542505194
Chromosome Location	chr3:48469826-48469827
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	chr3:48469776-48471162	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48468563-48472948	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:48468603-48471989	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYBL2	chr3:48469649-48470371	HepG2	liver:	n/a	n/a
5	CREB1	chr3:48469743-48473462	HepG2	liver:	n/a	n/a
6	TAF1	chr3:48469762-48471869	H1-hESC	embryonic stem cell:	n/a	n/a
7	EP300	chr3:48469805-48470566	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:48466790-48473062	HepG2	liver:	n/a	n/a
9	HEY1	chr3:48469646-48472042	HepG2	liver:	n/a	chr3:48471229-48471244 chr3:48470221-48470236 chr3:48470955-48470970 chr3:48470572-48470587 chr3:48471347-48471362 chr3:48470953-48470968
10	POLR2A	chr3:48466636-48473218	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:48461949-48470573	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:48469739-48471688	H1-neurons	neurons:	n/a	n/a
13	HEY1	chr3:48469356-48473141	HepG2	liver:	n/a	chr3:48471229-48471244 chr3:48470221-48470236 chr3:48470955-48470970 chr3:48470572-48470587 chr3:48471347-48471362 chr3:48470953-48470968
14	POLR2A	chr3:48469811-48471766	H1-neurons	neurons:	n/a	n/a
15	TAF1	chr3:48469764-48470158	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:48469582-48472048	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr3:48469799-48470156	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZEB1	chr3:48469774-48473492	HepG2	liver:	n/a	chr3:48471157-48471164 chr3:48471410-48471422
19	POLR2A	chr3:48469652-48471931	HepG2	liver:	n/a	n/a
20	YY1	chr3:48469727-48471920	HepG2	liver:	n/a	chr3:48471050-48471064 chr3:48471056-48471065 chr3:48470955-48470969 chr3:48471230-48471241
21	SIN3A	chr3:48469738-48472007	H1-hESC	embryonic stem cell:	n/a	chr3:48471240-48471249 chr3:48471333-48471342
22	ZNF263	chr3:48468929-48470023	HEK293-T-REx	kidney:	n/a	n/a
23	REST	chr3:48469446-48471910	H1-neurons	neurons:	n/a	chr3:48471333-48471343 chr3:48471343-48471356 chr3:48469903-48469913 chr3:48470943-48470956 chr3:48469907-48469916 chr3:48471255-48471262 chr3:48470994-48471012
24	TAF1	chr3:48469779-48471852	HepG2	liver:	n/a	n/a
25	TBP	chr3:48469800-48471835	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD2	chr3:48469631-48470083	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:48469643-48471881	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAZ	chr3:48469476-48472061	IMR90	lung:	n/a	chr3:48471053-48471063 chr3:48471085-48471094 chr3:48471081-48471090 chr3:48470436-48470446 chr3:48471214-48471224
29	POLR2A	chr3:48469824-48472480	HepG2	liver:	n/a	n/a
30	NFIC	chr3:48469726-48470136	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:48466832-48470960	HepG2	liver:	n/a	n/a
32	NR2F2	chr3:48469324-48473447	HepG2	liver:	n/a	n/a
33	MYBL2	chr3:48469516-48470352	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:48469699-48470934	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48468692..48470258-chr3:48540999..48543179,2	K562	blood:
2	chr3:48447403..48451386-chr3:48469064..48473166,5	MCF-7	breast:
3	chr3:48468569..48471339-chr3:48481498..48483135,2	MCF-7	breast:
4	chr2:241503199..241505771-chr3:48469733..48471743,2	MCF-7	breast:
5	chr3:48469539..48472280-chr3:48487900..48489460,2	MCF-7	breast:
6	chr3:48468825..48473989-chr3:48477233..48479904,8	MCF-7	breast:
7	chr3:48454313..48457718-chr3:48468090..48471775,3	MCF-7	breast:
8	chr3:48449321..48451479-chr3:48469134..48470813,2	K562	blood:
9	chr3:48262147..48265261-chr3:48469207..48471708,3	MCF-7	breast:
10	chr3:48469238..48470766-chr3:48475328..48477578,2	K562	blood:
11	chr3:48342140..48344321-chr3:48467110..48469904,2	K562	blood:
12	chr3:48341872..48344261-chr3:48469680..48472661,4	MCF-7	breast:
13	chr3:48281213..48283691-chr3:48469389..48472428,3	K562	blood:
14	chr3:48468360..48471756-chr3:48485148..48489754,5	K562	blood:
15	chr3:48301212..48303241-chr3:48468487..48470721,2	MCF-7	breast:
16	chr3:48282380..48283987-chr3:48469620..48473031,3	MCF-7	breast:
17	chr3:48469445..48473059-chr3:48486174..48489531,5	MCF-7	breast:

Variant related genes	Relation type
PLXNB1	TF binding region
ENSG00000164053	Chromatin interaction
ENSG00000164047	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000142327	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000172113	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	esv3345173	chr3:48469473-48472321	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48466200-48470000	Enhancers	Spleen	Spleen
2	chr3:48466400-48470000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:48466400-48470000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr3:48466600-48470000	Enhancers	Placenta	Placenta
5	chr3:48466800-48470000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:48466800-48470200	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr3:48467000-48470000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr3:48467000-48470000	Flanking Active TSS	Colon Smooth Muscle	Colon
9	chr3:48467200-48470000	Flanking Active TSS	HSMMtube	muscle
10	chr3:48467200-48470200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:48467400-48470000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:48467800-48471400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr3:48468000-48470000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:48468000-48470000	Flanking Active TSS	Ovary	ovary
15	chr3:48468000-48470200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:48468000-48471400	Active TSS	Brain Cingulate Gyrus	brain
17	chr3:48468200-48470000	Flanking Active TSS	Liver	Liver
18	chr3:48468200-48470000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:48468200-48470200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:48468200-48470200	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr3:48468400-48470200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr3:48468600-48470000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:48468600-48470000	Flanking Active TSS	Colonic Mucosa	Colon
24	chr3:48468600-48470000	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr3:48468600-48470000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr3:48468600-48470200	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr3:48468600-48470200	Flanking Active TSS	HSMM	muscle
28	chr3:48468600-48472000	Active TSS	Fetal Kidney	kidney
29	chr3:48468800-48470000	Flanking Active TSS	Fetal Brain Male	brain
30	chr3:48468800-48470000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
31	chr3:48468800-48470000	Flanking Active TSS	Pancreas	Pancrea
32	chr3:48468800-48470000	Flanking Active TSS	NHDF-Ad	bronchial
33	chr3:48468800-48471800	Active TSS	Aorta	Aorta
34	chr3:48468800-48472000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr3:48469000-48470000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr3:48469000-48470000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:48469000-48470000	Flanking Active TSS	Fetal Heart	heart
38	chr3:48469000-48470000	Flanking Active TSS	Fetal Lung	lung
39	chr3:48469000-48470000	Flanking Active TSS	Hela-S3	cervix
40	chr3:48469000-48470200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:48469000-48470200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:48469000-48471600	Active TSS	Brain Angular Gyrus	brain
43	chr3:48469200-48470000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr3:48469200-48470000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr3:48469200-48470000	Flanking Active TSS	A549	lung
46	chr3:48469200-48470200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:48469200-48470200	Flanking Active TSS	NH-A	brain
48	chr3:48469400-48470000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr3:48469400-48470000	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr3:48469400-48470200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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