Variant report

Variant	rs567082409
Chromosome Location	chr4:75023867-75023868
allele	A/G
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	SIN3AK20	chr4:75023176-75024249	HCT-116	colon:	n/a	n/a
2	SIN3A	chr4:75023740-75024477	GM12878	blood:	n/a	chr4:75024028-75024041
3	YY1	chr4:75023484-75024359	GM12878	blood:	n/a	chr4:75023644-75023658 chr4:75024007-75024021 chr4:75023570-75023584 chr4:75024006-75024020 chr4:75023646-75023655 chr4:75024151-75024165 chr4:75024016-75024030
4	TCF12	chr4:75023349-75024066	ECC-1	luminal epithelium:	n/a	n/a
5	BHLHE40	chr4:75023367-75024606	GM12878	blood:	n/a	chr4:75023644-75023660 chr4:75024010-75024026 chr4:75024026-75024042 chr4:75024005-75024021
6	POLR2A	chr4:75023261-75024021	K562	blood:	n/a	n/a
7	BCLAF1	chr4:75023212-75023918	K562	blood:	n/a	n/a
8	MYC	chr4:75023345-75024393	K562	blood:	n/a	chr4:75024298-75024309 chr4:75024298-75024308 chr4:75024299-75024309 chr4:75024297-75024310 chr4:75024299-75024306 chr4:75024295-75024310 chr4:75024297-75024307 chr4:75024300-75024309 chr4:75024297-75024310 chr4:75024297-75024312 chr4:75024299-75024308 chr4:75024298-75024309 chr4:75024298-75024307 chr4:75024298-75024309
9	SMC3	chr4:75023738-75023968	GM12878	blood:	n/a	n/a
10	MYBL2	chr4:75023272-75023986	HepG2	liver:	n/a	n/a
11	YY1	chr4:75023625-75024062	GM12892	blood:	n/a	chr4:75023644-75023658 chr4:75024007-75024021 chr4:75024006-75024020 chr4:75023646-75023655 chr4:75024016-75024030
12	E2F6	chr4:75023402-75024378	K562	blood:	n/a	chr4:75023646-75023655 chr4:75023641-75023651
13	ATF3	chr4:75023411-75023934	A549	lung:	n/a	chr4:75023646-75023655
14	TAF1	chr4:75023397-75024034	SK-N-SH	brain:	n/a	n/a
15	SP1	chr4:75023374-75024041	K562	blood:	n/a	chr4:75023646-75023655 chr4:75023773-75023785 chr4:75023644-75023656 chr4:75023645-75023655 chr4:75023645-75023655 chr4:75023645-75023659 chr4:75023773-75023785 chr4:75023645-75023654 chr4:75023770-75023784 chr4:75023644-75023656 chr4:75023645-75023654
16	MAX	chr4:75023292-75024431	HepG2	liver:	n/a	chr4:75024298-75024309 chr4:75024298-75024308 chr4:75024299-75024309 chr4:75024297-75024310 chr4:75024299-75024306 chr4:75024295-75024310 chr4:75024297-75024307 chr4:75024300-75024309 chr4:75024297-75024310 chr4:75024297-75024312 chr4:75024299-75024308 chr4:75024298-75024309 chr4:75024298-75024307 chr4:75024298-75024309
17	MYC	chr4:75023366-75023916	MCF10A-Er-Src	breast:	n/a	n/a
18	HDAC2	chr4:75023507-75023891	K562	blood:	n/a	n/a
19	MXI1	chr4:75023021-75023940	K562	blood:	n/a	n/a
20	NR2F2	chr4:75023366-75024019	K562	blood:	n/a	n/a
21	POLR2A	chr4:75022946-75024297	K562	blood:	n/a	n/a
22	POLR2A	chr4:75022991-75025136	PBDE	blood:	n/a	n/a
23	CTCF	chr4:75023820-75023970	GM12868	blood:	n/a	n/a
24	CHD1	chr4:75023604-75024854	GM12878	blood:	n/a	n/a
25	MAX	chr4:75023358-75024474	HUVEC	blood vessel:	n/a	chr4:75024298-75024309 chr4:75024298-75024308 chr4:75024299-75024309 chr4:75024297-75024310 chr4:75024299-75024306 chr4:75024295-75024310 chr4:75024297-75024307 chr4:75024300-75024309 chr4:75024297-75024310 chr4:75024297-75024312 chr4:75024299-75024308 chr4:75024298-75024309 chr4:75024298-75024307 chr4:75024298-75024309
26	TEAD4	chr4:75023354-75024064	ECC-1	luminal epithelium:	n/a	n/a
27	TAF7	chr4:75023307-75024048	H1-hESC	embryonic stem cell:	n/a	n/a
28	HDAC2	chr4:75023398-75024136	H1-hESC	embryonic stem cell:	n/a	n/a
29	RUNX3	chr4:75023409-75024383	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:75023432-75024344	GM12891	blood:	n/a	n/a
31	POLR2A	chr4:75023343-75024299	NB4	blood:	n/a	n/a
32	ZBTB7A	chr4:75023516-75024170	K562	blood:	n/a	n/a
33	EP300	chr4:75022852-75023944	K562	blood:	n/a	n/a
34	SMARCB1	chr4:75023477-75024309	Hela-S3	cervix:	n/a	n/a
35	REST	chr4:75022921-75024668	H1-neurons	neurons:	n/a	chr4:75023676-75023696 chr4:75024016-75024026 chr4:75023771-75023784 chr4:75023682-75023696 chr4:75023645-75023658
36	GABPA	chr4:75023336-75024201	K562	blood:	n/a	chr4:75024010-75024019 chr4:75023646-75023655
37	POLR2A	chr4:75023430-75024385	GM12892	blood:	n/a	n/a
38	CREB1	chr4:75023309-75024124	HepG2	liver:	n/a	n/a
39	BCL3	chr4:75023580-75024083	GM12878	blood:	n/a	chr4:75024006-75024019 chr4:75024013-75024026
40	TBL1XR1	chr4:75023543-75023993	K562	blood:	n/a	n/a
41	MAX	chr4:75023347-75024435	H1-hESC	embryonic stem cell:	n/a	chr4:75024298-75024309 chr4:75024298-75024308 chr4:75024299-75024309 chr4:75024297-75024310 chr4:75024299-75024306 chr4:75024295-75024310 chr4:75024297-75024307 chr4:75024300-75024309 chr4:75024297-75024310 chr4:75024297-75024312 chr4:75024299-75024308 chr4:75024298-75024309 chr4:75024298-75024307 chr4:75024298-75024309
42	FOSL2	chr4:75023326-75023975	HepG2	liver:	n/a	n/a
43	HCFC1	chr4:75022751-75025210	Hela-S3	cervix:	n/a	n/a
44	MAX	chr4:75023314-75024474	H1-hESC	embryonic stem cell:	n/a	chr4:75024298-75024309 chr4:75024298-75024308 chr4:75024299-75024309 chr4:75024297-75024310 chr4:75024299-75024306 chr4:75024295-75024310 chr4:75024297-75024307 chr4:75024300-75024309 chr4:75024297-75024310 chr4:75024297-75024312 chr4:75024299-75024308 chr4:75024298-75024309 chr4:75024298-75024307 chr4:75024298-75024309
45	RELA	chr4:75023298-75024328	GM15510	blood:	n/a	n/a
46	USF1	chr4:75023544-75023880	A549	lung:	n/a	chr4:75023644-75023660
47	NFIC	chr4:75023237-75024109	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr4:75023459-75024012	GM12891	blood:	n/a	n/a
49	POLR2A	chr4:75022866-75024826	GM12891	blood:	n/a	n/a
50	POLR2A	chr4:75023316-75024013	SK-N-MC	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:75023851-75023901	GM19239	blood:	n/a
2	chr4:75023849-75023899	ovcar-3	ovarian:	n/a
3	chr4:75023849-75023899	ECC-1	luminal epithelium:	n/a
4	chr4:75023849-75023899	AG04449	skin:	fetal
5	chr4:75023851-75023901	HNPCEpiC	eye:	n/a
6	chr4:75023849-75023899	SAEC	small airway:	n/a
7	chr4:75023851-75023901	Hela-S3	cervix:	n/a
8	chr4:75023851-75023901	SAEC	small airway:	n/a
9	chr4:75023849-75023899	RPTEC	kidney:	n/a
10	chr4:75023851-75023901	RPTEC	kidney:	n/a
11	chr4:75023849-75023899	HRPEpiC	eye:	n/a
12	chr4:75023849-75023899	GM12878	blood:	n/a
13	chr4:75023849-75023899	Hela-S3	cervix:	n/a
14	chr4:75023851-75023901	T-47D	breast:	n/a
15	chr4:75023849-75023899	Caco-2	colon:	n/a
16	chr4:75023851-75023901	HL-60	blood:	n/a
17	chr4:75023851-75023901	Jurkat	blood:	n/a
18	chr4:75023849-75023899	HEK293	kidney:	embryo
19	chr4:75023849-75023899	HUVEC	blood vessel:	n/a
20	chr4:75023851-75023901	SKMC	muscle:	n/a
21	chr4:75023849-75023899	PrEC	prostate:	n/a
22	chr4:75023851-75023901	GM12878	blood:	n/a
23	chr4:75023849-75023899	HPAEpiC	pulmonary alveolar:	n/a
24	chr4:75023851-75023901	AG09309	skin:	n/a
25	chr4:75023851-75023901	Hepatocyte	liver:	n/a
26	chr4:75023849-75023899	GM06990	blood:	n/a
27	chr4:75023851-75023901	Caco-2	colon:	n/a
28	chr4:75023851-75023901	NH-A	brain:	n/a
29	chr4:75023849-75023899	K562	blood:	n/a
30	chr4:75023851-75023901	SK-N-MC	brain:	n/a
31	chr4:75023849-75023899	ProgFib	skin:	n/a
32	chr4:75023849-75023899	Hepatocyte	liver:	n/a
33	chr4:75023849-75023899	T-47D	breast:	n/a
34	chr4:75023849-75023899	SK-N-MC	brain:	n/a
35	chr4:75023851-75023901	NHBE	bronchial:	n/a
36	chr4:75023851-75023901	HCM	heart:	n/a
37	chr4:75023849-75023899	A549	lung:	n/a
38	chr4:75023851-75023901	PANC-1	pancreas:	n/a
39	chr4:75023851-75023901	U87	brain:	n/a
40	chr4:75023851-75023901	BJ	skin:	n/a
41	chr4:75023849-75023899	HCT-116	colon:	n/a
42	chr4:75023849-75023899	AoSMC	blood vessel:	n/a
43	chr4:75023851-75023901	AG04449	skin:	fetal
44	chr4:75023851-75023901	HRPEpiC	eye:	n/a
45	chr4:75023851-75023901	AG10803	skin:	n/a
46	chr4:75023851-75023901	MCF-7	breast:	n/a
47	chr4:75023851-75023901	ECC-1	luminal epithelium:	n/a
48	chr4:75023849-75023899	U87	brain:	n/a
49	chr4:75023851-75023901	HMEC	breast:	n/a
50	chr4:75023851-75023901	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:74964506..74967065-chr4:75022087..75025561,3	K562	blood:
2	chr4:75023679..75024199-chr6:117923622..117924531,2	NB4	blood:
3	chr4:74122515..74124717-chr4:75023066..75024638,2	K562	blood:
4	chr4:75023332..75025369-chr4:75145514..75147366,2	MCF-7	breast:
5	chr4:75022872..75025434-chr4:75174456..75176612,2	MCF-7	breast:
6	chr1:45196394..45197102-chr4:75023670..75024212,2	Hela-S3	cervix:
7	chr4:74920487..74923421-chr4:75023614..75026198,3	K562	blood:
8	chr20:277413..278096-chr4:75023404..75023960,2	NB4	blood:
9	chr4:75023432..75024127-chr7:115891562..115892062,2	NB4	blood:
10	chr4:74964506..74968474-chr4:75022087..75025768,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPGN-4	chr4:75023829-75023998	NONHSAT096885

Variant related genes	Relation type
MTHFD2L	TF binding region
MTHFD2L	CpG island
ENSG00000177764	Chromatin interaction
ENSG00000047932	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000182585	Chromatin interaction
ENSG00000132466	Chromatin interaction
ENSG00000163738	Chromatin interaction
ENSG00000081041	Chromatin interaction
ENSG00000135269	Chromatin interaction
ENSG00000248848	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv594683	chr4:75013441-75106485	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594684	chr4:75015750-75106485	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3346537	chr4:75022913-75025461	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr4:75022600-75025000	Active TSS	K562	blood
2	chr4:75022800-75024600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:75022800-75025200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:75022800-75025200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:75022800-75025400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:75023000-75024400	Active TSS	Fetal Brain Female	brain
7	chr4:75023000-75024600	Active TSS	Stomach Mucosa	stomach
8	chr4:75023000-75024800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:75023000-75024800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:75023000-75024800	Active TSS	Colonic Mucosa	Colon
11	chr4:75023000-75025000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr4:75023000-75025000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:75023000-75025000	Active TSS	Fetal Muscle Trunk	muscle
14	chr4:75023000-75025000	Active TSS	Fetal Stomach	stomach
15	chr4:75023000-75025000	Active TSS	HepG2	liver
16	chr4:75023000-75025200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr4:75023000-75025200	Active TSS	Thymus	Thymus
18	chr4:75023000-75025800	Active TSS	A549	lung
19	chr4:75023200-75024400	Active TSS	Fetal Brain Male	brain
20	chr4:75023200-75024400	Active TSS	Placenta Amnion	Placenta Amnion
21	chr4:75023200-75024600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:75023200-75024600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr4:75023200-75024600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:75023200-75024600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:75023200-75024600	Active TSS	Brain Anterior Caudate	brain
26	chr4:75023200-75024600	Active TSS	Rectal Smooth Muscle	rectum
27	chr4:75023200-75024800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:75023200-75024800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:75023200-75024800	Active TSS	Left Ventricle	heart
30	chr4:75023200-75024800	Active TSS	Ovary	ovary
31	chr4:75023200-75024800	Active TSS	Pancreas	Pancrea
32	chr4:75023200-75025000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:75023200-75025000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:75023200-75025000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:75023200-75025200	Active TSS	Aorta	Aorta
36	chr4:75023200-75025200	Active TSS	Fetal Intestine Large	intestine
37	chr4:75023200-75025200	Active TSS	Fetal Intestine Small	intestine
38	chr4:75023200-75025400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:75023200-75025400	Active TSS	Psoas Muscle	Psoas
40	chr4:75023200-75025400	Active TSS	Right Ventricle	heart
41	chr4:75023400-75024200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr4:75023400-75024200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:75023400-75024400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:75023400-75024400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:75023400-75024400	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr4:75023400-75024400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:75023400-75024400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:75023400-75024400	Active TSS	Brain Angular Gyrus	brain
49	chr4:75023400-75024400	Active TSS	Brain Substantia Nigra	brain
50	chr4:75023400-75024400	Active TSS	Colon Smooth Muscle	Colon

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