Variant report

Variant	rs2023532
Chromosome Location	chr4:103747541-103747542
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	POLR2A	chr4:103747377-103749984	HL-60	blood:	n/a	n/a
2	BCLAF1	chr4:103747444-103750011	GM12878	blood:	n/a	chr4:103748724-103748733 chr4:103749806-103749815
3	POLR2A	chr4:103746212-103750739	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr4:103746375-103750078	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr4:103746789-103749912	GM12891	blood:	n/a	n/a
6	NFATC1	chr4:103747332-103749923	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:103747341-103749909	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr4:103747489-103749826	GM12878	blood:	n/a	n/a
9	POLR2A	chr4:103746714-103750026	GM12892	blood:	n/a	n/a
10	HEY1	chr4:103746870-103750013	K562	blood:	n/a	chr4:103748332-103748347
11	POLR2A	chr4:103746216-103750681	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:103746462-103750746	K562	blood:	n/a	n/a
13	POLR2A	chr4:103747444-103750188	HepG2	liver:	n/a	n/a
14	POLR2A	chr4:103746464-103750001	PBDE	blood:	n/a	n/a
15	CHD1	chr4:103746270-103750377	GM12878	blood:	n/a	chr4:103748391-103748401 chr4:103748142-103748152 chr4:103747370-103747377
16	POLR2A	chr4:103746817-103750738	K562	blood:	n/a	n/a
17	POLR2A	chr4:103747511-103749964	K562	blood:	n/a	n/a
18	MXI1	chr4:103745018-103750658	IMR90	lung:	n/a	n/a
19	POLR2A	chr4:103747503-103747766	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:103746932-103750611	Raji	blood:	n/a	n/a
21	POLR2A	chr4:103746794-103750731	GM12892	blood:	n/a	n/a
22	POLR2A	chr4:103747407-103747753	HepG2	liver:	n/a	n/a
23	POLR2A	chr4:103744252-103750750	K562	blood:	n/a	n/a
24	MXI1	chr4:103744961-103750789	SK-N-SH	brain:	n/a	n/a
25	PML	chr4:103746399-103750687	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:103746396-103750745	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:103746977-103749916	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:103747500-103749885	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr4:103746615-103749905	GM18505	blood:	n/a	n/a
30	POLR2A	chr4:103747390-103749949	HL-60	blood:	n/a	n/a
31	POLR2A	chr4:103747512-103749825	HepG2	liver:	n/a	n/a
32	POLR2A	chr4:103747535-103749831	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr4:103747453-103749906	K562	blood:	n/a	n/a
34	YY1	chr4:103747455-103749794	GM12878	blood:	n/a	n/a
35	CHD1	chr4:103743990-103750660	IMR90	lung:	n/a	chr4:103748391-103748401 chr4:103748142-103748152 chr4:103747370-103747377
36	POLR2A	chr4:103747401-103750695	Hela-S3	cervix:	n/a	n/a
37	STAT5A	chr4:103747493-103749845	GM12878	blood:	n/a	chr4:103748184-103748195 chr4:103748548-103748560 chr4:103748931-103748943 chr4:103748725-103748737 chr4:103748024-103748036 chr4:103748926-103748938
38	SIN3A	chr4:103746330-103749916	H1-hESC	embryonic stem cell:	n/a	chr4:103748885-103748893 chr4:103748507-103748518
39	POLR2A	chr4:103746677-103750737	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr4:103747518-103749810	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr4:103746966-103749839	GM12892	blood:	n/a	n/a
42	POLR2A	chr4:103746320-103749952	HUVEC	blood vessel:	n/a	n/a
43	MAZ	chr4:103746338-103749987	IMR90	lung:	n/a	chr4:103748924-103748934 chr4:103749588-103749599 chr4:103749588-103749599 chr4:103749061-103749070 chr4:103749590-103749597 chr4:103749589-103749598
44	POLR2A	chr4:103746790-103750076	H1-hESC	embryonic stem cell:	n/a	n/a
45	WRNIP1	chr4:103746595-103749882	GM12878	blood:	n/a	n/a
46	POLR2A	chr4:103747493-103749827	GM12878	blood:	n/a	n/a
47	CHD1	chr4:103745496-103750418	H1-hESC	embryonic stem cell:	n/a	chr4:103748391-103748401 chr4:103748142-103748152 chr4:103747370-103747377
48	FOXM1	chr4:103747517-103749923	GM12878	blood:	n/a	n/a
49	IRF1	chr4:103745748-103747544	K562	blood:	n/a	chr4:103746101-103746115
50	POLR2A	chr4:103747375-103749950	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103419348..103423957-chr4:103746554..103750456,7	MCF-7	breast:
2	chr4:103730843..103736706-chr4:103746374..103749972,8	MCF-7	breast:
3	chr4:103421566..103424767-chr4:103746039..103749014,5	K562	blood:
4	chr4:103747245..103749359-chr4:103986696..103989097,2	K562	blood:
5	chr4:103264289..103266526-chr4:103747342..103750313,2	K562	blood:
6	chr4:103747527..103750862-chr4:103937830..103941231,4	MCF-7	breast:
7	chr4:103747144..103749225-chr4:103996606..103998315,2	K562	blood:
8	chr4:103650888..103653325-chr4:103747345..103748932,2	MCF-7	breast:
9	chr4:103746553..103755574-chr4:103787108..103794302,29	MCF-7	breast:
10	chr4:103680041..103683633-chr4:103747125..103750295,6	MCF-7	breast:
11	chr4:103723421..103727498-chr4:103747024..103749804,3	MCF-7	breast:
12	chr4:103721670..103724216-chr4:103745688..103748268,3	MCF-7	breast:
13	chr4:103747413..103749606-chr4:103996961..103999341,3	MCF-7	breast:
14	chr4:103745482..103752084-chr4:103788371..103792114,20	MCF-7	breast:
15	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
16	chr4:100871315..100874297-chr4:103746830..103749271,3	K562	blood:
17	chr4:103422194..103424603-chr4:103745115..103749014,4	K562	blood:
18	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:

Variant related genes	Relation type
UBE2D3	TF binding region
ENSG00000246560	TF binding region
ENSG00000230069	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000164037	Chromatin interaction
ENSG00000238948	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000109323	Chromatin interaction
ENSG00000138821	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000260651	Chromatin interaction
ENSG00000248971	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000164038	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10005010	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap]
rs10025625	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10033243	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17033384	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs17256589	0.83[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs2198199	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs3774997	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap]
rs3960787	0.83[CEU][hapmap];0.82[GIH][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	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2023532	TET2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103742000-103750200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr4:103742600-103748400	Active TSS	Right Atrium	heart
3	chr4:103742800-103747800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:103742800-103748000	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr4:103742800-103748800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:103743200-103750000	Active TSS	Aorta	Aorta
7	chr4:103743400-103748200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:103743600-103750200	Active TSS	NHLF	lung
9	chr4:103744000-103750400	Active TSS	Right Ventricle	heart
10	chr4:103744200-103747800	Transcr. at gene 5' and 3'	Osteobl	bone
11	chr4:103744200-103748200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
12	chr4:103744200-103748800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:103744200-103749600	Active TSS	Primary T cells fromperipheralblood	blood
14	chr4:103744400-103747800	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:103744400-103748600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
16	chr4:103744400-103750000	Active TSS	Ovary	ovary
17	chr4:103744400-103750200	Active TSS	Left Ventricle	heart
18	chr4:103744400-103750200	Active TSS	HSMMtube	muscle
19	chr4:103744400-103750400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:103744600-103749600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:103744600-103749600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:103744800-103747800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:103744800-103750400	Active TSS	Colonic Mucosa	Colon
24	chr4:103744800-103750600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:103745000-103749800	Active TSS	Lung	lung
26	chr4:103745000-103750000	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr4:103745000-103750200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:103745200-103750200	Active TSS	HMEC	breast
29	chr4:103745200-103750200	Active TSS	NHDF-Ad	bronchial
30	chr4:103745200-103750400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr4:103745400-103749800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:103745400-103749800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:103745400-103749800	Active TSS	Stomach Smooth Muscle	stomach
34	chr4:103745400-103750200	Active TSS	A549	lung
35	chr4:103745400-103750200	Active TSS	Hela-S3	cervix
36	chr4:103745400-103750400	Active TSS	GM12878-XiMat	blood
37	chr4:103745400-103750800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr4:103745600-103749800	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr4:103745600-103750000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr4:103745800-103748000	Transcr. at gene 5' and 3'	Fetal Lung	lung
41	chr4:103745800-103748600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr4:103745800-103749600	Active TSS	Adipose Nuclei	Adipose
43	chr4:103745800-103749600	Active TSS	Placenta	Placenta
44	chr4:103745800-103749600	Active TSS	NH-A	brain
45	chr4:103745800-103749800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:103745800-103750000	Active TSS	Fetal Muscle Trunk	muscle
47	chr4:103745800-103750200	Active TSS	Fetal Intestine Large	intestine
48	chr4:103745800-103750200	Active TSS	Psoas Muscle	Psoas
49	chr4:103745800-103750400	Active TSS	H1 Cell Line	embryonic stem cell
50	chr4:103745800-103750400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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