Variant report

Variant	rs9880242
Chromosome Location	chr3:111805120-111805121
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:184)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:184 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr3:111805018-111805398	Hela-S3	cervix:	n/a	n/a
2	SP4	chr3:111804980-111805491	H1-hESC	embryonic stem cell:	n/a	n/a
3	RFX5	chr3:111805079-111805807	Hela-S3	cervix:	n/a	n/a
4	MYC	chr3:111805073-111805446	MCF-7	breast:	n/a	n/a
5	MXI1	chr3:111805082-111805488	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:111804892-111805608	A549	lung:	n/a	n/a
7	NANOG	chr3:111805051-111805391	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZBTB7A	chr3:111805052-111805279	K562	blood:	n/a	n/a
9	POLR2A	chr3:111805054-111805603	K562	blood:	n/a	n/a
10	POLR2A	chr3:111804936-111805640	ProgFib	skin:	n/a	n/a
11	POLR2A	chr3:111805047-111805536	MCF-7	breast:	n/a	n/a
12	POLR2A	chr3:111804843-111805908	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3A	chr3:111804692-111805955	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:111804940-111805587	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr3:111804951-111805493	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:111805061-111805632	Hela-S3	cervix:	n/a	n/a
17	MAX	chr3:111804434-111805924	HCT-116	colon:	n/a	n/a
18	POLR2A	chr3:111805043-111805463	U87	brain:	n/a	n/a
19	POLR2A	chr3:111805004-111805506	A549	lung:	n/a	n/a
20	MAX	chr3:111804610-111805427	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYBL2	chr3:111805090-111805496	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:111804781-111805787	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIN3AK20	chr3:111805094-111805702	PANC-1	pancreas:	n/a	n/a
24	MAZ	chr3:111804824-111805614	GM12878	blood:	n/a	n/a
25	TAF1	chr3:111805027-111805464	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr3:111805064-111805867	Hela-S3	cervix:	n/a	n/a
27	ZBTB7A	chr3:111804843-111805744	ECC-1	luminal epithelium:	n/a	n/a
28	E2F6	chr3:111804773-111805702	A549	lung:	n/a	chr3:111805424-111805434
29	JUND	chr3:111804990-111805474	A549	lung:	n/a	n/a
30	BHLHE40	chr3:111805111-111805377	K562	blood:	n/a	n/a
31	TAF1	chr3:111804960-111805657	A549	lung:	n/a	n/a
32	POLR2A	chr3:111804946-111806681	IMR90	lung:	n/a	n/a
33	JUND	chr3:111805088-111805791	K562	blood:	n/a	n/a
34	MAX	chr3:111804578-111805684	K562	blood:	n/a	n/a
35	TCF7L2	chr3:111805103-111805698	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr3:111804993-111805566	HUVEC	blood vessel:	n/a	n/a
37	TCF12	chr3:111804691-111805653	A549	lung:	n/a	n/a
38	UBTF	chr3:111804969-111805638	K562	blood:	n/a	n/a
39	CHD2	chr3:111805026-111805670	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:111804995-111805744	Hela-S3	cervix:	n/a	n/a
41	TBP	chr3:111805064-111805598	K562	blood:	n/a	n/a
42	CREB1	chr3:111804719-111805817	H1-hESC	embryonic stem cell:	n/a	n/a
43	CREB1	chr3:111804955-111805623	A549	lung:	n/a	n/a
44	MAX	chr3:111804944-111805645	SK-N-SH	brain:	n/a	n/a
45	TCF7L2	chr3:111805078-111805443	HCT-116	colon:	n/a	n/a
46	JUND	chr3:111804973-111805682	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chr3:111805099-111805439	GM12878	blood:	n/a	n/a
48	TAF1	chr3:111804866-111805664	ECC-1	luminal epithelium:	n/a	n/a
49	RCOR1	chr3:111805040-111805691	Hela-S3	cervix:	n/a	n/a
50	ELF1	chr3:111805030-111805274	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:111805077-111805127	Caco-2	colon:	n/a
2	chr3:111805077-111805127	GM12878	blood:	n/a
3	chr3:111805077-111805127	ovcar-3	ovarian:	n/a
4	chr3:111805077-111805127	HCT-116	colon:	n/a
5	chr3:111805077-111805127	HRE	kidney:	n/a
6	chr3:111805077-111805127	NHBE	bronchial:	n/a
7	chr3:111805077-111805127	AG09309	skin:	n/a
8	chr3:111805077-111805127	LNCaP	prostate:	n/a
9	chr3:111805077-111805127	RPTEC	kidney:	n/a
10	chr3:111805077-111805127	PFSK-1	brain:	n/a
11	chr3:111805077-111805127	HEK293	kidney:	embryo
12	chr3:111805077-111805127	HIPEpiC	eye:	n/a
13	chr3:111805077-111805127	BJ	skin:	n/a
14	chr3:111805077-111805127	MCF-7	breast:	n/a
15	chr3:111805077-111805127	PrEC	prostate:	n/a
16	chr3:111805077-111805127	K562	blood:	n/a
17	chr3:111805077-111805127	H1-hESC	embryonic stem cell:	embryo
18	chr3:111805077-111805127	SK-N-SH	brain:	n/a
19	chr3:111805077-111805127	SAEC	small airway:	n/a
20	chr3:111805077-111805127	CMK	blood:	n/a
21	chr3:111805077-111805127	U87	brain:	n/a
22	chr3:111805077-111805127	AoSMC	blood vessel:	n/a
23	chr3:111805077-111805127	HepG2	liver:	n/a
24	chr3:111805077-111805127	HRCEpiC	kidney:	n/a
25	chr3:111805077-111805127	AG09319	gingival:	n/a
26	chr3:111805077-111805127	NB4	blood:	n/a
27	chr3:111805077-111805127	MCF10A-Er-Src	breast:	n/a
28	chr3:111805077-111805127	HCF	heart:	n/a
29	chr3:111805077-111805127	GM12892	blood:	n/a
30	chr3:111805077-111805127	HEEpiC	esophagus:	n/a
31	chr3:111805077-111805127	SK-N-SH_RA	brain:	n/a
32	chr3:111805077-111805127	GM19239	blood:	n/a
33	chr3:111805077-111805127	HAEpiC	amniotic membrane:	n/a
34	chr3:111805077-111805127	HCM	heart:	n/a
35	chr3:111805077-111805127	GM12891	blood:	n/a
36	chr3:111805077-111805127	SK-N-MC	brain:	n/a
37	chr3:111805077-111805127	BE2_C	brain:	n/a
38	chr3:111805077-111805127	Hepatocyte	liver:	n/a
39	chr3:111805077-111805127	AG10803	skin:	n/a
40	chr3:111805077-111805127	HPAEpiC	pulmonary alveolar:	n/a
41	chr3:111805077-111805127	T-47D	breast:	n/a
42	chr3:111805077-111805127	HUVEC	blood vessel:	n/a
43	chr3:111805077-111805127	GM06990	blood:	n/a
44	chr3:111805077-111805127	AG04450	lung:	fetal
45	chr3:111805077-111805127	NHDF-neo	bronchial:	n/a
46	chr3:111805077-111805127	Jurkat	blood:	n/a
47	chr3:111805077-111805127	AG04449	skin:	fetal
48	chr3:111805077-111805127	NT2-D1	testis:	n/a
49	chr3:111805077-111805127	HMEC	breast:	n/a
50	chr3:111805077-111805127	Hela-S3	cervix:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111803332..111805315-chr3:112279253..112281220,2	MCF-7	breast:
2	chr15:59225042..59225969-chr3:111804939..111805795,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
C3orf52	TF binding region
C3orf52	CpG island
ENSG00000138459	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1492488	0.86[ASW][hapmap]
rs16859274	1.00[MEX][hapmap]
rs4682362	1.00[MEX][hapmap]
rs7649379	0.86[ASW][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755927	chr3:111794310-111834310	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9880242	C3orf52	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111804400-111805200	Flanking Active TSS	Fetal Thymus	thymus
2	chr3:111804600-111805200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:111804600-111805200	Flanking Active TSS	Pancreas	Pancrea
4	chr3:111804600-111805200	Flanking Active TSS	HMEC	breast
5	chr3:111804600-111805600	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr3:111804600-111805800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:111804600-111805800	Active TSS	Brain Anterior Caudate	brain
8	chr3:111804600-111805800	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:111804600-111806000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr3:111804600-111806000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:111804600-111806000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:111804600-111806000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:111804600-111806000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:111804600-111806000	Active TSS	Brain Cingulate Gyrus	brain
15	chr3:111804600-111806000	Active TSS	Fetal Kidney	kidney
16	chr3:111804600-111806000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr3:111804600-111806400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:111804600-111806600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:111804600-111806800	Active TSS	Rectal Smooth Muscle	rectum
20	chr3:111804800-111805200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr3:111804800-111805200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:111804800-111805200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr3:111804800-111805200	Flanking Active TSS	Colonic Mucosa	Colon
24	chr3:111804800-111805400	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr3:111804800-111805400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:111804800-111805400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:111804800-111805400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:111804800-111805600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr3:111804800-111805600	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr3:111804800-111805600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:111804800-111805600	Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:111804800-111805600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:111804800-111805800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
34	chr3:111804800-111805800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
35	chr3:111804800-111805800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
36	chr3:111804800-111805800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:111804800-111805800	Flanking Active TSS	Liver	Liver
38	chr3:111804800-111805800	Active TSS	Brain Angular Gyrus	brain
39	chr3:111804800-111805800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:111804800-111805800	Active TSS	Colon Smooth Muscle	Colon
41	chr3:111804800-111805800	Active TSS	Esophagus	oesophagus
42	chr3:111804800-111805800	Active TSS	Left Ventricle	heart
43	chr3:111804800-111805800	Active TSS	Lung	lung
44	chr3:111804800-111805800	Active TSS	Ovary	ovary
45	chr3:111804800-111805800	Active TSS	Psoas Muscle	Psoas
46	chr3:111804800-111805800	Enhancers	Spleen	Spleen
47	chr3:111804800-111805800	Active TSS	HSMM	muscle
48	chr3:111804800-111805800	Active TSS	HSMMtube	muscle
49	chr3:111804800-111806000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:111804800-111806000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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