Variant report

Variant	rs3774997
Chromosome Location	chr4:103746753-103746754
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	TRIM28	chr4:103746251-103747224	K562	blood:	n/a	n/a
2	ELF1	chr4:103746548-103747273	MCF-7	breast:	n/a	chr4:103747021-103747034 chr4:103747022-103747033
3	MAX	chr4:103746312-103747176	NB4	blood:	n/a	n/a
4	NFIC	chr4:103746476-103747403	GM12878	blood:	n/a	n/a
5	HCFC1	chr4:103746512-103747222	K562	blood:	n/a	n/a
6	ZNF143	chr4:103746488-103747063	GM12878	blood:	n/a	n/a
7	EP300	chr4:103746288-103747331	K562	blood:	n/a	chr4:103746753-103746766 chr4:103747042-103747049
8	POLR2A	chr4:103746555-103747246	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr4:103746212-103750739	MCF10A-Er-Src	breast:	n/a	n/a
10	RUNX3	chr4:103746463-103747177	GM12878	blood:	n/a	n/a
11	YY1	chr4:103746365-103747193	SK-N-SH_RA	brain:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691
12	TEAD4	chr4:103746394-103747202	K562	blood:	n/a	n/a
13	MYC	chr4:103746457-103747511	NB4	blood:	n/a	n/a
14	YY1	chr4:103746228-103747383	SK-N-SH	brain:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691
15	YY1	chr4:103746501-103746897	K562	blood:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691
16	POLR2A	chr4:103746317-103747301	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr4:103746375-103750078	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr4:103746714-103750026	GM12892	blood:	n/a	n/a
19	BHLHE40	chr4:103746544-103747064	GM12878	blood:	n/a	n/a
20	YY1	chr4:103746376-103747083	H1-hESC	embryonic stem cell:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691
21	POLR2A	chr4:103746216-103750681	GM12878	blood:	n/a	n/a
22	GABPA	chr4:103746672-103747265	A549	lung:	n/a	n/a
23	BHLHE40	chr4:103746540-103747142	K562	blood:	n/a	n/a
24	POLR2A	chr4:103746462-103750746	K562	blood:	n/a	n/a
25	GABPA	chr4:103746650-103747302	SK-N-SH	brain:	n/a	n/a
26	EP300	chr4:103746654-103747049	H1-hESC	embryonic stem cell:	n/a	chr4:103746753-103746766 chr4:103747042-103747049
27	SIN3AK20	chr4:103746752-103747460	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr4:103746464-103750001	PBDE	blood:	n/a	n/a
29	CHD1	chr4:103746270-103750377	GM12878	blood:	n/a	chr4:103748391-103748401 chr4:103748142-103748152 chr4:103747370-103747377
30	YY1	chr4:103746570-103746757	HCT-116	colon:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691
31	MXI1	chr4:103745018-103750658	IMR90	lung:	n/a	n/a
32	CEBPB	chr4:103746189-103746904	A549	lung:	n/a	chr4:103746479-103746490 chr4:103746480-103746489 chr4:103746478-103746491
33	CTCF	chr4:103746720-103746870	BE2_C	brain:	n/a	n/a
34	TBL1XR1	chr4:103745937-103747238	K562	blood:	n/a	n/a
35	YY1	chr4:103746333-103746830	GM12892	blood:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691
36	CEBPB	chr4:103746104-103746979	HCT-116	colon:	n/a	chr4:103746479-103746490 chr4:103746480-103746489 chr4:103746478-103746491
37	CEBPB	chr4:103746291-103747133	A549	lung:	n/a	chr4:103746479-103746490 chr4:103746480-103746489 chr4:103746478-103746491
38	CEBPB	chr4:103746279-103747124	H1-hESC	embryonic stem cell:	n/a	chr4:103746479-103746490 chr4:103746480-103746489 chr4:103746478-103746491
39	MXI1	chr4:103746344-103747238	K562	blood:	n/a	n/a
40	STAT3	chr4:103746332-103747185	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr4:103744252-103750750	K562	blood:	n/a	n/a
42	MXI1	chr4:103744961-103750789	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr4:103746634-103747206	HUVEC	blood vessel:	n/a	n/a
44	CEBPB	chr4:103746321-103746879	HCT-116	colon:	n/a	chr4:103746479-103746490 chr4:103746480-103746489 chr4:103746478-103746491
45	YY1	chr4:103746266-103747269	SK-N-SH	brain:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691
46	YY1	chr4:103746425-103747122	A549	lung:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691
47	POLR2A	chr4:103746511-103746789	HepG2	liver:	n/a	n/a
48	PML	chr4:103746399-103750687	GM12878	blood:	n/a	n/a
49	POLR2A	chr4:103746556-103747324	H1-hESC	embryonic stem cell:	n/a	n/a
50	YY1	chr4:103746470-103746871	GM12891	blood:	n/a	chr4:103746681-103746693 chr4:103746682-103746704 chr4:103746682-103746692 chr4:103746683-103746691

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	chr4:103746553..103755574-chr4:103787108..103794302,29	MCF-7	breast:
5	chr4:103680426..103684137-chr4:103744957..103747230,3	K562	blood:
6	chr4:103721670..103724216-chr4:103745688..103748268,3	MCF-7	breast:
7	chr4:103745482..103752084-chr4:103788371..103792114,20	MCF-7	breast:
8	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
9	chr4:103422194..103424603-chr4:103745115..103749014,4	K562	blood:
10	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:

Variant related genes	Relation type
ENSG00000246560	TF binding region
UBE2D3	TF binding region
ENSG00000238948	Chromatin interaction
ENSG00000109323	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction
ENSG00000145354	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];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap]
rs10025625	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs10033243	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap]
rs17033384	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs17256589	0.94[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]
rs2023532	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap]
rs2198199	0.89[ASW][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap]
rs3960787	0.94[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][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
rs3774997	TET2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103740800-103747200	Transcr. at gene 5' and 3'	K562	blood
2	chr4:103742000-103750200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr4:103742600-103748400	Active TSS	Right Atrium	heart
4	chr4:103742800-103747800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:103742800-103748000	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr4:103742800-103748800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:103743200-103747200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr4:103743200-103750000	Active TSS	Aorta	Aorta
9	chr4:103743400-103748200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:103743600-103750200	Active TSS	NHLF	lung
11	chr4:103744000-103747400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
12	chr4:103744000-103750400	Active TSS	Right Ventricle	heart
13	chr4:103744200-103747000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
14	chr4:103744200-103747800	Transcr. at gene 5' and 3'	Osteobl	bone
15	chr4:103744200-103748200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
16	chr4:103744200-103748800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:103744200-103749600	Active TSS	Primary T cells fromperipheralblood	blood
18	chr4:103744400-103746800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:103744400-103747800	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:103744400-103748600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
21	chr4:103744400-103750000	Active TSS	Ovary	ovary
22	chr4:103744400-103750200	Active TSS	Left Ventricle	heart
23	chr4:103744400-103750200	Active TSS	HSMMtube	muscle
24	chr4:103744400-103750400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:103744600-103747200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:103744600-103749600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:103744600-103749600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:103744800-103747800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:103744800-103750400	Active TSS	Colonic Mucosa	Colon
30	chr4:103744800-103750600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:103745000-103749800	Active TSS	Lung	lung
32	chr4:103745000-103750000	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr4:103745000-103750200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:103745200-103750200	Active TSS	HMEC	breast
35	chr4:103745200-103750200	Active TSS	NHDF-Ad	bronchial
36	chr4:103745200-103750400	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr4:103745400-103749800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:103745400-103749800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:103745400-103749800	Active TSS	Stomach Smooth Muscle	stomach
40	chr4:103745400-103750200	Active TSS	A549	lung
41	chr4:103745400-103750200	Active TSS	Hela-S3	cervix
42	chr4:103745400-103750400	Active TSS	GM12878-XiMat	blood
43	chr4:103745400-103750800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr4:103745600-103746800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr4:103745600-103747000	Active TSS	Fetal Stomach	stomach
46	chr4:103745600-103749800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr4:103745600-103750000	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr4:103745800-103746800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
49	chr4:103745800-103746800	Weak transcription	Spleen	Spleen
50	chr4:103745800-103747200	Active TSS	Fetal Intestine Small	intestine

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