Variant report

Variant	rs9872722
Chromosome Location	chr3:48470535-48470536
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	SMARCB1	chr3:48470467-48472003	Hela-S3	cervix:	n/a	n/a
2	SP1	chr3:48469885-48470538	HepG2	liver:	n/a	chr3:48469926-48469933 chr3:48470395-48470404 chr3:48470391-48470405
3	MAZ	chr3:48470389-48471701	GM12878	blood:	n/a	chr3:48471053-48471063 chr3:48471085-48471094 chr3:48471081-48471090 chr3:48470436-48470446 chr3:48471214-48471224
4	POLR2A	chr3:48470293-48471960	MCF-7	breast:	n/a	n/a
5	CCNT2	chr3:48470530-48471636	K562	blood:	n/a	chr3:48471021-48471030
6	POLR2A	chr3:48469776-48471162	HepG2	liver:	n/a	n/a
7	JUND	chr3:48470329-48470537	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:48468563-48472948	H1-hESC	embryonic stem cell:	n/a	n/a
9	HCFC1	chr3:48470290-48472076	Hela-S3	cervix:	n/a	n/a
10	ZBTB7A	chr3:48469998-48470537	HepG2	liver:	n/a	chr3:48470440-48470449
11	POLR2A	chr3:48468603-48471989	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF7L2	chr3:48470454-48471743	HCT-116	colon:	n/a	n/a
13	MAX	chr3:48470516-48471796	K562	blood:	n/a	chr3:48471053-48471063 chr3:48471085-48471094 chr3:48471081-48471090 chr3:48471214-48471224
14	POLR2A	chr3:48470371-48471682	HCT-116	colon:	n/a	n/a
15	CREB1	chr3:48469743-48473462	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:48470264-48471113	HUVEC	blood vessel:	n/a	n/a
17	CHD2	chr3:48470350-48470790	HepG2	liver:	n/a	chr3:48470442-48470452
18	TAF1	chr3:48469762-48471869	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAF1	chr3:48470268-48471327	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr3:48470301-48472065	MCF-7	breast:	n/a	n/a
21	EP300	chr3:48469805-48470566	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:48470263-48471902	MCF-7	breast:	n/a	n/a
23	POLR2A	chr3:48466790-48473062	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:48470504-48471900	NB4	blood:	n/a	n/a
25	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
26	POLR2A	chr3:48466636-48473218	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:48461949-48470573	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:48470276-48470695	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr3:48470451-48471239	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr3:48470449-48470579	Gliobla	brain:	n/a	n/a
31	POLR2A	chr3:48470404-48470680	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr3:48469739-48471688	H1-neurons	neurons:	n/a	n/a
33	POLR2A	chr3:48470093-48471731	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr3:48470228-48471896	HepG2	liver:	n/a	n/a
35	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
36	GABPA	chr3:48470524-48471240	H1-hESC	embryonic stem cell:	n/a	n/a
37	HNF4A	chr3:48469866-48470567	HepG2	liver:	n/a	n/a
38	MAZ	chr3:48469896-48472124	HepG2	liver:	n/a	chr3:48471053-48471063 chr3:48471085-48471094 chr3:48471081-48471090 chr3:48470436-48470446 chr3:48471214-48471224
39	POLR2A	chr3:48469811-48471766	H1-neurons	neurons:	n/a	n/a
40	TAF7	chr3:48470396-48470931	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:48469582-48472048	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr3:48470461-48471419	GM18951	blood:	n/a	n/a
43	ZBTB7A	chr3:48469893-48470665	HepG2	liver:	n/a	chr3:48470440-48470449
44	CEBPD	chr3:48469856-48470725	HepG2	liver:	n/a	n/a
45	TBP	chr3:48469856-48470965	HepG2	liver:	n/a	n/a
46	POLR2A	chr3:48470273-48471251	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr3:48470308-48471942	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr3:48470442-48471812	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr3:48470431-48471123	IMR90	lung:	n/a	n/a
50	POLR2A	chr3:48470279-48470686	SK-N-SH	brain:	n/a	n/a

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

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

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13433990	1.00[AFR][1000 genomes]
rs28607362	1.00[AFR][1000 genomes]
rs9829727	0.87[AFR][1000 genomes]
rs9848493	1.00[AFR][1000 genomes]

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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48467800-48471400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr3:48468000-48471400	Active TSS	Brain Cingulate Gyrus	brain
3	chr3:48468600-48472000	Active TSS	Fetal Kidney	kidney
4	chr3:48468800-48471800	Active TSS	Aorta	Aorta
5	chr3:48468800-48472000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:48469000-48471600	Active TSS	Brain Angular Gyrus	brain
7	chr3:48469400-48471600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:48469600-48471400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:48469600-48471800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:48469800-48470600	Flanking Bivalent TSS/Enh	Dnd41	blood
11	chr3:48469800-48471200	Active TSS	Primary T cells from cord blood	blood
12	chr3:48469800-48471200	Active TSS	Brain Substantia Nigra	brain
13	chr3:48469800-48471200	Active TSS	HMEC	breast
14	chr3:48469800-48471400	Active TSS	Brain Hippocampus Middle	brain
15	chr3:48469800-48471400	Active TSS	Placenta Amnion	Placenta Amnion
16	chr3:48469800-48471600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:48469800-48471600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:48469800-48471600	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr3:48469800-48471600	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr3:48469800-48471600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr3:48469800-48471600	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr3:48469800-48471600	Active TSS	Rectal Smooth Muscle	rectum
23	chr3:48469800-48471600	Active TSS	Small Intestine	intestine
24	chr3:48469800-48471600	Active TSS	HepG2	liver
25	chr3:48469800-48471800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr3:48469800-48472000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr3:48469800-48472400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr3:48470000-48470600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:48470000-48470800	Active TSS	Brain Germinal Matrix	brain
30	chr3:48470000-48471000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:48470000-48471200	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:48470000-48471200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:48470000-48471200	Active TSS	Brain Anterior Caudate	brain
34	chr3:48470000-48471200	Active TSS	Colonic Mucosa	Colon
35	chr3:48470000-48471200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr3:48470000-48471200	Weak transcription	Fetal Heart	heart
37	chr3:48470000-48471200	Weak transcription	Stomach Mucosa	stomach
38	chr3:48470000-48471200	Active TSS	HSMMtube	muscle
39	chr3:48470000-48471400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:48470000-48471400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:48470000-48471400	Active TSS	Esophagus	oesophagus
42	chr3:48470000-48471400	Active TSS	Psoas Muscle	Psoas
43	chr3:48470000-48471400	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:48470000-48471400	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr3:48470000-48471400	Active TSS	A549	lung
46	chr3:48470000-48471400	Active TSS	NHDF-Ad	bronchial
47	chr3:48470000-48471400	Active TSS	Osteobl	bone
48	chr3:48470000-48471600	Active TSS	H1 Cell Line	embryonic stem cell
49	chr3:48470000-48471600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:48470000-48471600	Active TSS	HUES6 Cell Line	embryonic stem cell

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