Variant report

Variant	rs575809192
Chromosome Location	chr3:48471235-48471236
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	NFIC	chr3:48470938-48472194	ECC-1	luminal epithelium:	n/a	chr3:48471952-48471968 chr3:48471952-48471969
2	CHD2	chr3:48471070-48471745	HepG2	liver:	n/a	chr3:48471346-48471356 chr3:48471140-48471150 chr3:48471341-48471351
3	CHD2	chr3:48470675-48471919	H1-hESC	embryonic stem cell:	n/a	chr3:48471346-48471356 chr3:48471140-48471150 chr3:48471341-48471351
4	TCF12	chr3:48470933-48472100	ECC-1	luminal epithelium:	n/a	chr3:48471803-48471810
5	TAF7	chr3:48471089-48471883	H1-hESC	embryonic stem cell:	n/a	n/a
6	SMARCB1	chr3:48470467-48472003	Hela-S3	cervix:	n/a	n/a
7	NFIC	chr3:48470856-48472274	ECC-1	luminal epithelium:	n/a	chr3:48471952-48471968 chr3:48471952-48471969
8	MAZ	chr3:48470389-48471701	GM12878	blood:	n/a	chr3:48471053-48471063 chr3:48471085-48471094 chr3:48471081-48471090 chr3:48470436-48470446 chr3:48471214-48471224
9	POLR2A	chr3:48470293-48471960	MCF-7	breast:	n/a	n/a
10	ELF1	chr3:48470590-48471322	GM12878	blood:	n/a	chr3:48471000-48471012 chr3:48471211-48471223
11	EP300	chr3:48470921-48471916	HepG2	liver:	n/a	n/a
12	CCNT2	chr3:48470530-48471636	K562	blood:	n/a	chr3:48471021-48471030
13	POLR2A	chr3:48470768-48471876	K562	blood:	n/a	n/a
14	GABPA	chr3:48470804-48471301	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:48471220-48471485	ProgFib	skin:	n/a	n/a
16	POLR2A	chr3:48468563-48472948	H1-hESC	embryonic stem cell:	n/a	n/a
17	ELF1	chr3:48470827-48471764	K562	blood:	n/a	chr3:48471000-48471012 chr3:48471211-48471223
18	HCFC1	chr3:48470290-48472076	Hela-S3	cervix:	n/a	n/a
19	MXI1	chr3:48470999-48471715	Hela-S3	cervix:	n/a	chr3:48471079-48471094 chr3:48471081-48471096
20	POLR2A	chr3:48468603-48471989	H1-hESC	embryonic stem cell:	n/a	n/a
21	GABPA	chr3:48470978-48471834	MCF-7	breast:	n/a	chr3:48471348-48471357
22	ZEB1	chr3:48470955-48471637	GM12878	blood:	n/a	chr3:48471157-48471164 chr3:48471410-48471422
23	POLR2A	chr3:48470630-48471771	Hela-S3	cervix:	n/a	n/a
24	RCOR1	chr3:48471157-48472144	Hela-S3	cervix:	n/a	n/a
25	EGR1	chr3:48470887-48471318	ECC-1	luminal epithelium:	n/a	chr3:48471054-48471067 chr3:48471054-48471067 chr3:48471057-48471067 chr3:48471057-48471066 chr3:48471054-48471068 chr3:48471055-48471069 chr3:48471054-48471067 chr3:48471050-48471072 chr3:48471052-48471062 chr3:48471054-48471067 chr3:48471053-48471068
26	RCOR1	chr3:48470676-48471823	HepG2	liver:	n/a	n/a
27	MYC	chr3:48470666-48471780	H1-hESC	embryonic stem cell:	n/a	chr3:48471053-48471063 chr3:48471085-48471094 chr3:48471081-48471090 chr3:48471214-48471224
28	TCF7L2	chr3:48470454-48471743	HCT-116	colon:	n/a	n/a
29	MAX	chr3:48470516-48471796	K562	blood:	n/a	chr3:48471053-48471063 chr3:48471085-48471094 chr3:48471081-48471090 chr3:48471214-48471224
30	POLR2A	chr3:48470371-48471682	HCT-116	colon:	n/a	n/a
31	CREB1	chr3:48469743-48473462	HepG2	liver:	n/a	n/a
32	GABPA	chr3:48470840-48471347	Hela-S3	cervix:	n/a	n/a
33	TCF12	chr3:48471034-48471297	GM12878	blood:	n/a	n/a
34	TAF1	chr3:48469762-48471869	H1-hESC	embryonic stem cell:	n/a	n/a
35	TAF1	chr3:48470268-48471327	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr3:48470301-48472065	MCF-7	breast:	n/a	n/a
37	POLR2A	chr3:48470263-48471902	MCF-7	breast:	n/a	n/a
38	POLR2A	chr3:48466790-48473062	HepG2	liver:	n/a	n/a
39	POLR2A	chr3:48471203-48471926	HepG2	liver:	n/a	n/a
40	MYBL2	chr3:48470906-48472265	HepG2	liver:	n/a	n/a
41	YY1	chr3:48470713-48471790	ECC-1	luminal epithelium:	n/a	chr3:48471050-48471064 chr3:48471056-48471065 chr3:48470955-48470969 chr3:48471230-48471241
42	POLR2A	chr3:48470504-48471900	NB4	blood:	n/a	n/a
43	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
44	CEBPD	chr3:48470744-48471949	HepG2	liver:	n/a	n/a
45	ELF1	chr3:48470736-48471699	K562	blood:	n/a	chr3:48471000-48471012 chr3:48471211-48471223
46	POLR2A	chr3:48471102-48471291	GM12878	blood:	n/a	n/a
47	ELF1	chr3:48470791-48471305	HepG2	liver:	n/a	chr3:48471000-48471012 chr3:48471211-48471223
48	POLR2A	chr3:48466636-48473218	HepG2	liver:	n/a	n/a
49	FOXA2	chr3:48471014-48472106	HepG2	liver:	n/a	n/a
50	EGR1	chr3:48470756-48471302	H1-hESC	embryonic stem cell:	n/a	chr3:48471054-48471067 chr3:48471054-48471067 chr3:48471057-48471067 chr3:48471057-48471066 chr3:48471054-48471068 chr3:48471055-48471069 chr3:48471054-48471067 chr3:48471050-48471072 chr3:48471052-48471062 chr3:48471054-48471067 chr3:48471053-48471068

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48471233-48471283	NHDF-neo	bronchial:	n/a
2	chr3:48471218-48471268	U87	brain:	n/a
3	chr3:48471218-48471268	Jurkat	blood:	n/a
4	chr3:48471218-48471268	HRPEpiC	eye:	n/a
5	chr3:48471233-48471283	PFSK-1	brain:	n/a
6	chr3:48471233-48471283	HMEC	breast:	n/a
7	chr3:48471218-48471268	RPTEC	kidney:	n/a
8	chr3:48471233-48471283	A549	lung:	n/a
9	chr3:48471218-48471268	SK-N-SH	brain:	n/a
10	chr3:48471233-48471283	IMR90	lung:	fetal
11	chr3:48471233-48471283	GM06990	blood:	n/a
12	chr3:48471233-48471283	Caco-2	colon:	n/a
13	chr3:48471218-48471268	HNPCEpiC	eye:	n/a
14	chr3:48471218-48471268	NHDF-neo	bronchial:	n/a
15	chr3:48471218-48471268	HEEpiC	esophagus:	n/a
16	chr3:48471233-48471283	HRPEpiC	eye:	n/a
17	chr3:48471233-48471283	SK-N-SH	brain:	n/a
18	chr3:48471233-48471283	Jurkat	blood:	n/a
19	chr3:48471233-48471283	HUVEC	blood vessel:	n/a
20	chr3:48471233-48471283	AG10803	skin:	n/a
21	chr3:48471218-48471268	HEK293	kidney:	embryo
22	chr3:48471218-48471268	AG04449	skin:	fetal
23	chr3:48471218-48471268	PANC-1	pancreas:	n/a
24	chr3:48471233-48471283	HCPEpiC	choroid plexus:	n/a
25	chr3:48471218-48471268	HMEC	breast:	n/a
26	chr3:48471233-48471283	HCT-116	colon:	n/a
27	chr3:48471233-48471283	HAEpiC	amniotic membrane:	n/a
28	chr3:48471218-48471268	GM12892	blood:	n/a
29	chr3:48471233-48471283	AG04450	lung:	fetal
30	chr3:48471233-48471283	Hela-S3	cervix:	n/a
31	chr3:48471218-48471268	HPAEpiC	pulmonary alveolar:	n/a
32	chr3:48471233-48471283	HL-60	blood:	n/a
33	chr3:48471233-48471283	ovcar-3	ovarian:	n/a
34	chr3:48471218-48471268	CMK	blood:	n/a
35	chr3:48471233-48471283	H1-hESC	embryonic stem cell:	embryo
36	chr3:48471218-48471268	MCF-7	breast:	n/a
37	chr3:48471218-48471268	IMR90	lung:	fetal
38	chr3:48471218-48471268	Hela-S3	cervix:	n/a
39	chr3:48471233-48471283	NB4	blood:	n/a
40	chr3:48471233-48471283	ProgFib	skin:	n/a
41	chr3:48471218-48471268	K562	blood:	n/a
42	chr3:48471218-48471268	HL-60	blood:	n/a
43	chr3:48471233-48471283	NH-A	brain:	n/a
44	chr3:48471218-48471268	HUVEC	blood vessel:	n/a
45	chr3:48471233-48471283	RPTEC	kidney:	n/a
46	chr3:48471218-48471268	PrEC	prostate:	n/a
47	chr3:48471233-48471283	SK-N-MC	brain:	n/a
48	chr3:48471218-48471268	HIPEpiC	eye:	n/a
49	chr3:48471218-48471268	GM12891	blood:	n/a
50	chr3:48471218-48471268	GM19239	blood:	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	chr3:48282088..48283714-chr3:48470890..48472488,2	MCF-7	breast:
8	chr3:48262147..48265261-chr3:48469207..48471708,3	MCF-7	breast:
9	chr3:48341872..48344261-chr3:48469680..48472661,4	MCF-7	breast:
10	chr3:48281213..48283691-chr3:48469389..48472428,3	K562	blood:
11	chr3:48468360..48471756-chr3:48485148..48489754,5	K562	blood:
12	chr3:48470951..48473880-chr3:48506965..48509988,4	MCF-7	breast:
13	chr3:48282380..48283987-chr3:48469620..48473031,3	MCF-7	breast:
14	chr1:8937871..8938802-chr3:48470851..48471584,2	Hela-S3	cervix:
15	chr3:48469445..48473059-chr3:48486174..48489531,5	MCF-7	breast:

Variant related genes	Relation type
PLXNB1	TF binding region
PLXNB1	CpG island
ENSG00000172113	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000074800	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000164047	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000236269	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000142327	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000164051	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:127 , 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	chr3:48469800-48471400	Active TSS	Brain Hippocampus Middle	brain
11	chr3:48469800-48471400	Active TSS	Placenta Amnion	Placenta Amnion
12	chr3:48469800-48471600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:48469800-48471600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:48469800-48471600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:48469800-48471600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:48469800-48471600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr3:48469800-48471600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:48469800-48471600	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:48469800-48471600	Active TSS	Small Intestine	intestine
20	chr3:48469800-48471600	Active TSS	HepG2	liver
21	chr3:48469800-48471800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:48469800-48472000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr3:48469800-48472400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr3:48470000-48471400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:48470000-48471400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:48470000-48471400	Active TSS	Esophagus	oesophagus
27	chr3:48470000-48471400	Active TSS	Psoas Muscle	Psoas
28	chr3:48470000-48471400	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr3:48470000-48471400	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr3:48470000-48471400	Active TSS	A549	lung
31	chr3:48470000-48471400	Active TSS	NHDF-Ad	bronchial
32	chr3:48470000-48471400	Active TSS	Osteobl	bone
33	chr3:48470000-48471600	Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:48470000-48471600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:48470000-48471600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr3:48470000-48471600	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr3:48470000-48471600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:48470000-48471600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:48470000-48471600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:48470000-48471600	Active TSS	Liver	Liver
41	chr3:48470000-48471600	Active TSS	Colon Smooth Muscle	Colon
42	chr3:48470000-48471600	Active TSS	Fetal Intestine Large	intestine
43	chr3:48470000-48471600	Active TSS	Fetal Intestine Small	intestine
44	chr3:48470000-48471600	Active TSS	Fetal Lung	lung
45	chr3:48470000-48471600	Active TSS	Gastric	stomach
46	chr3:48470000-48471600	Active TSS	Lung	lung
47	chr3:48470000-48471600	Active TSS	Ovary	ovary
48	chr3:48470000-48471600	Active TSS	Pancreas	Pancrea
49	chr3:48470000-48471600	Active TSS	Right Atrium	heart
50	chr3:48470000-48471600	Active TSS	GM12878-XiMat	blood

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