Variant report

Variant	rs538054141
Chromosome Location	chr3:138664357-138664358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr3:138663792-138664456	K562	blood:	n/a	n/a
2	UBTF	chr3:138662706-138664404	K562	blood:	n/a	n/a
3	RCOR1	chr3:138662698-138664470	K562	blood:	n/a	n/a
4	UBTF	chr3:138661738-138664476	K562	blood:	n/a	n/a
5	CREB1	chr3:138664085-138664600	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:138664281-138664501	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:138663614-138664596	K562	blood:	n/a	n/a
8	MAX	chr3:138663821-138666675	K562	blood:	n/a	chr3:138666114-138666124
9	E2F6	chr3:138663661-138666655	H1-hESC	embryonic stem cell:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
10	MAX	chr3:138663718-138664693	K562	blood:	n/a	n/a
11	MYC	chr3:138664085-138664434	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:138663620-138664574	K562	blood:	n/a	n/a
13	SETDB1	chr3:138663779-138665311	K562	blood:	n/a	n/a
14	GTF2F1	chr3:138664101-138664549	H1-hESC	embryonic stem cell:	n/a	n/a
15	ATF3	chr3:138664245-138664490	K562	blood:	n/a	n/a
16	POLR2A	chr3:138663600-138664417	K562	blood:	n/a	n/a
17	SUZ12	chr3:138663787-138664668	H1-hESC	embryonic stem cell:	n/a	n/a
18	CCNT2	chr3:138663704-138666364	K562	blood:	n/a	chr3:138665889-138665898 chr3:138665882-138665891
19	MAX	chr3:138663637-138666899	K562	blood:	n/a	chr3:138666114-138666124
20	CBX3	chr3:138663708-138664570	K562	blood:	n/a	n/a
21	NR2F2	chr3:138663127-138664535	K562	blood:	n/a	n/a
22	HCFC1	chr3:138663744-138664418	K562	blood:	n/a	n/a
23	TBP	chr3:138663828-138664440	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3A	chr3:138664143-138664503	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr3:138663680-138664627	H1-neurons	neurons:	n/a	n/a
26	MAX	chr3:138663689-138665507	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr3:138662909-138664407	K562	blood:	n/a	n/a
28	E2F6	chr3:138663622-138666590	K562	blood:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
29	MYC	chr3:138662705-138666843	K562	blood:	n/a	chr3:138666114-138666124
30	E2F6	chr3:138664155-138664554	K562	blood:	n/a	n/a
31	MAZ	chr3:138663646-138664435	K562	blood:	n/a	n/a
32	MAX	chr3:138663683-138666644	H1-hESC	embryonic stem cell:	n/a	chr3:138666114-138666124
33	ZNF143	chr3:138663713-138664479	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr3:138663930-138665344	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr3:138662764-138664435	K562	blood:	n/a	n/a
36	TCF12	chr3:138663993-138664456	H1-hESC	embryonic stem cell:	n/a	n/a
37	E2F6	chr3:138663731-138667013	K562	blood:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
38	POLR2A	chr3:138661932-138664635	H1-neurons	neurons:	n/a	n/a
39	HMGN3	chr3:138663651-138666531	K562	blood:	n/a	n/a
40	E2F6	chr3:138663107-138666566	H1-hESC	embryonic stem cell:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
41	NR2F2	chr3:138663741-138664444	K562	blood:	n/a	n/a
42	CREB1	chr3:138663899-138664564	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTBP2	chr3:138663148-138666770	H1-hESC	embryonic stem cell:	n/a	n/a
44	SUZ12	chr3:138662343-138670118	NT2-D1	testis:	n/a	n/a
45	TEAD4	chr3:138664200-138664611	H1-hESC	embryonic stem cell:	n/a	n/a
46	CHD2	chr3:138664310-138664482	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:138664350-138664400	Jurkat	blood:	n/a
2	chr3:138664350-138664400	GM06990	blood:	n/a
3	chr3:138664350-138664400	NHBE	bronchial:	n/a
4	chr3:138664350-138664400	HEEpiC	esophagus:	n/a
5	chr3:138664350-138664400	PANC-1	pancreas:	n/a
6	chr3:138664350-138664400	SKMC	muscle:	n/a
7	chr3:138664350-138664400	GM19239	blood:	n/a
8	chr3:138664350-138664400	BJ	skin:	n/a
9	chr3:138664350-138664400	NB4	blood:	n/a
10	chr3:138664350-138664400	A549	lung:	n/a
11	chr3:138664350-138664400	AG10803	skin:	n/a
12	chr3:138664350-138664400	MCF10A-Er-Src	breast:	n/a
13	chr3:138664350-138664400	ProgFib	skin:	n/a
14	chr3:138664350-138664400	HRE	kidney:	n/a
15	chr3:138664350-138664400	ECC-1	luminal epithelium:	n/a
16	chr3:138664350-138664400	HIPEpiC	eye:	n/a
17	chr3:138664350-138664400	HAEpiC	amniotic membrane:	n/a
18	chr3:138664350-138664400	AG04449	skin:	fetal
19	chr3:138664350-138664400	PrEC	prostate:	n/a
20	chr3:138664350-138664400	NHDF-neo	bronchial:	n/a
21	chr3:138664350-138664400	SK-N-MC	brain:	n/a
22	chr3:138664350-138664400	PFSK-1	brain:	n/a
23	chr3:138664350-138664400	Hela-S3	cervix:	n/a
24	chr3:138664350-138664400	SAEC	small airway:	n/a
25	chr3:138664350-138664400	MCF-7	breast:	n/a
26	chr3:138664350-138664400	GM12878	blood:	n/a
27	chr3:138664350-138664400	HCM	heart:	n/a
28	chr3:138664350-138664400	AG09309	skin:	n/a
29	chr3:138664350-138664400	GM12891	blood:	n/a
30	chr3:138664350-138664400	Hepatocyte	liver:	n/a
31	chr3:138664350-138664400	AG09319	gingival:	n/a
32	chr3:138664350-138664400	HUVEC	blood vessel:	n/a
33	chr3:138664350-138664400	LNCaP	prostate:	n/a
34	chr3:138664350-138664400	IMR90	lung:	fetal
35	chr3:138664350-138664400	NT2-D1	testis:	n/a
36	chr3:138664350-138664400	HEK293	kidney:	embryo
37	chr3:138664350-138664400	HRPEpiC	eye:	n/a
38	chr3:138664350-138664400	SK-N-SH	brain:	n/a
39	chr3:138664350-138664400	AoSMC	blood vessel:	n/a
40	chr3:138664350-138664400	AG04450	lung:	fetal
41	chr3:138664350-138664400	ovcar-3	ovarian:	n/a
42	chr3:138664350-138664400	T-47D	breast:	n/a
43	chr3:138664350-138664400	HCPEpiC	choroid plexus:	n/a
44	chr3:138664350-138664400	GM12892	blood:	n/a
45	chr3:138664350-138664400	U87	brain:	n/a
46	chr3:138664350-138664400	NH-A	brain:	n/a
47	chr3:138664350-138664400	SK-N-SH_RA	brain:	n/a
48	chr3:138664350-138664400	HCT-116	colon:	n/a
49	chr3:138664350-138664400	HL-60	blood:	n/a
50	chr3:138664350-138664400	HRCEpiC	kidney:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:138662930..138665142-chr3:139048462..139050899,2	K562	blood:
2	chr3:138663277..138665291-chr3:138920079..138922965,2	K562	blood:
3	chr3:138663376..138665458-chr3:138892996..138895666,2	K562	blood:
4	chr3:138661376..138665068-chr3:139062620..139064700,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244578	TF binding region
C3orf72	TF binding region
ENSG00000244578	CpG island
C3orf72	CpG island
ENSG00000175110	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv877540	chr3:138645013-138670695	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv877541	chr3:138645013-138673922	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv877542	chr3:138645013-138750904	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv3338518	chr3:138663787-138666635	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv530096	chr3:138664024-138665683	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138662400-138666600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:138662800-138666600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr3:138663000-138664600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
4	chr3:138663000-138664800	Weak transcription	A549	lung
5	chr3:138663000-138665000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
6	chr3:138663000-138665200	Bivalent Enhancer	Liver	Liver
7	chr3:138663000-138666400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:138663000-138666600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:138663000-138666600	Active TSS	Hela-S3	cervix
10	chr3:138663200-138664400	Bivalent Enhancer	Fetal Intestine Small	intestine
11	chr3:138663200-138664600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
12	chr3:138663200-138665200	Bivalent Enhancer	Placenta	Placenta
13	chr3:138663200-138666000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
14	chr3:138663200-138666000	Bivalent Enhancer	Small Intestine	intestine
15	chr3:138663400-138664600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
16	chr3:138663400-138664600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:138663400-138665200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr3:138663400-138665200	Bivalent Enhancer	Stomach Mucosa	stomach
19	chr3:138663400-138666400	Bivalent Enhancer	Fetal Brain Male	brain
20	chr3:138663400-138666600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr3:138663600-138664400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr3:138663600-138664400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:138663600-138664400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
24	chr3:138663600-138664400	Bivalent Enhancer	Fetal Heart	heart
25	chr3:138663600-138664400	Bivalent Enhancer	Fetal Thymus	thymus
26	chr3:138663600-138664600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
27	chr3:138663600-138664600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
28	chr3:138663600-138664600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:138663600-138665400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:138663600-138666400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:138663600-138666600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr3:138663600-138666600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr3:138663600-138666800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:138663800-138664400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
38	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
39	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
40	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
43	chr3:138663800-138664400	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
44	chr3:138663800-138664400	Bivalent/Poised TSS	HepG2	liver
45	chr3:138663800-138664600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
46	chr3:138663800-138664600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
47	chr3:138663800-138664600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:138663800-138664600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:138663800-138664600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:138663800-138664600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin

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