Variant report

Variant	rs574034893
Chromosome Location	chr3:142607812-142607813
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	GTF2F1	chr3:142606964-142608003	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:142606954-142608071	Hela-S3	cervix:	n/a	n/a
3	MAX	chr3:142606829-142608177	HCT-116	colon:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
4	REST	chr3:142607602-142607837	A549	lung:	n/a	n/a
5	MAX	chr3:142607125-142608144	SK-N-SH	brain:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
6	ZNF143	chr3:142607557-142607934	Hela-S3	cervix:	n/a	n/a
7	MAX	chr3:142606806-142608167	ECC-1	luminal epithelium:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
8	POLR2A	chr3:142607295-142608050	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF7L2	chr3:142607030-142608204	HCT-116	colon:	n/a	n/a
10	TBL1XR1	chr3:142607804-142607840	K562	blood:	n/a	n/a
11	MAX	chr3:142606853-142608072	Hela-S3	cervix:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
12	CTBP2	chr3:142607012-142608279	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr3:142606856-142608302	H1-hESC	embryonic stem cell:	n/a	chr3:142608047-142608057
14	E2F1	chr3:142607199-142608071	Hela-S3	cervix:	n/a	chr3:142607723-142607734 chr3:142608047-142608057
15	SMARCB1	chr3:142607002-142608275	Hela-S3	cervix:	n/a	n/a
16	MYC	chr3:142607241-142607858	MCF-7	breast:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
17	JUND	chr3:142607095-142607943	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr3:142607800-142607950	GM12873	blood:	n/a	n/a
19	POLR2A	chr3:142606943-142608096	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr3:142606972-142607916	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:142607029-142608091	H1-hESC	embryonic stem cell:	n/a	n/a
22	TBP	chr3:142606978-142608376	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:142607610-142607902	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:142607644-142608092	ProgFib	skin:	n/a	n/a
25	ZBTB7A	chr3:142607469-142608248	K562	blood:	n/a	chr3:142607642-142607651
26	TAF7	chr3:142606969-142608082	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr3:142607008-142608169	H1-hESC	embryonic stem cell:	n/a	n/a
28	RCOR1	chr3:142606813-142608044	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:142606946-142608115	Hela-S3	cervix:	n/a	n/a
30	MYC	chr3:142606855-142608204	A549	lung:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
31	MAX	chr3:142606984-142608208	NB4	blood:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
32	E2F6	chr3:142607114-142608109	K562	blood:	n/a	chr3:142608047-142608057
33	TAF1	chr3:142607798-142608021	SK-N-SH	brain:	n/a	n/a
34	MAX	chr3:142606830-142608243	A549	lung:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
35	RCOR1	chr3:142607644-142607990	HepG2	liver:	n/a	n/a
36	E2F6	chr3:142606919-142608092	H1-hESC	embryonic stem cell:	n/a	chr3:142608047-142608057
37	YY1	chr3:142607554-142608104	ECC-1	luminal epithelium:	n/a	n/a
38	MYC	chr3:142607132-142607870	K562	blood:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
39	POLR2A	chr3:142607319-142608120	A549	lung:	n/a	n/a
40	CREB1	chr3:142607682-142608148	A549	lung:	n/a	n/a
41	SMC3	chr3:142606932-142608036	Hela-S3	cervix:	n/a	chr3:142607390-142607404
42	SIN3A	chr3:142606970-142608279	H1-hESC	embryonic stem cell:	n/a	chr3:142607930-142607941 chr3:142607169-142607178
43	POLR2A	chr3:142607482-142608015	MCF-7	breast:	n/a	n/a
44	TAF1	chr3:142606915-142608073	A549	lung:	n/a	n/a
45	CTCF	chr3:142607740-142607890	AG04449	skin:	n/a	n/a
46	MYC	chr3:142607157-142607835	H1-hESC	embryonic stem cell:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
47	POLR2A	chr3:142606945-142608129	HCT-116	colon:	n/a	n/a
48	HA-E2F1	chr3:142607158-142608147	Hela-S3	cervix:	n/a	chr3:142607723-142607734 chr3:142608047-142608057
49	POLR2A	chr3:142606975-142608191	HEK293	kidney:	n/a	n/a
50	ZKSCAN1	chr3:142607070-142607963	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142607799-142607849	HRE	kidney:	n/a
2	chr3:142607799-142607849	NT2-D1	testis:	n/a
3	chr3:142607799-142607849	AG04450	lung:	fetal
4	chr3:142607799-142607849	U87	brain:	n/a
5	chr3:142607799-142607849	T-47D	breast:	n/a
6	chr3:142607799-142607849	A549	lung:	n/a
7	chr3:142607799-142607849	AoSMC	blood vessel:	n/a
8	chr3:142607799-142607849	HCM	heart:	n/a
9	chr3:142607799-142607849	IMR90	lung:	fetal
10	chr3:142607799-142607849	GM12891	blood:	n/a
11	chr3:142607799-142607849	AG09309	skin:	n/a
12	chr3:142607799-142607849	GM12878	blood:	n/a
13	chr3:142607799-142607849	HUVEC	blood vessel:	n/a
14	chr3:142607799-142607849	HEEpiC	esophagus:	n/a
15	chr3:142607799-142607849	HCPEpiC	choroid plexus:	n/a
16	chr3:142607799-142607849	HL-60	blood:	n/a
17	chr3:142607799-142607849	GM06990	blood:	n/a
18	chr3:142607799-142607849	NB4	blood:	n/a
19	chr3:142607799-142607849	K562	blood:	n/a
20	chr3:142607799-142607849	PrEC	prostate:	n/a
21	chr3:142607799-142607849	ECC-1	luminal epithelium:	n/a
22	chr3:142607799-142607849	ovcar-3	ovarian:	n/a
23	chr3:142607799-142607849	PANC-1	pancreas:	n/a
24	chr3:142607799-142607849	Hela-S3	cervix:	n/a
25	chr3:142607799-142607849	PFSK-1	brain:	n/a
26	chr3:142607799-142607849	GM19239	blood:	n/a
27	chr3:142607799-142607849	HRPEpiC	eye:	n/a
28	chr3:142607799-142607849	BE2_C	brain:	n/a
29	chr3:142607799-142607849	HCF	heart:	n/a
30	chr3:142607799-142607849	HNPCEpiC	eye:	n/a
31	chr3:142607799-142607849	LNCaP	prostate:	n/a
32	chr3:142607799-142607849	RPTEC	kidney:	n/a
33	chr3:142607799-142607849	Caco-2	colon:	n/a
34	chr3:142607799-142607849	SAEC	small airway:	n/a
35	chr3:142607799-142607849	SKMC	muscle:	n/a
36	chr3:142607799-142607849	GM12892	blood:	n/a
37	chr3:142607799-142607849	HAEpiC	amniotic membrane:	n/a
38	chr3:142607799-142607849	Hepatocyte	liver:	n/a
39	chr3:142607799-142607849	SK-N-MC	brain:	n/a
40	chr3:142607799-142607849	NH-A	brain:	n/a
41	chr3:142607799-142607849	H1-hESC	embryonic stem cell:	embryo
42	chr3:142607799-142607849	MCF-7	breast:	n/a
43	chr3:142607799-142607849	AG10803	skin:	n/a
44	chr3:142607799-142607849	HIPEpiC	eye:	n/a
45	chr3:142607799-142607849	AG09319	gingival:	n/a
46	chr3:142607799-142607849	NHBE	bronchial:	n/a
47	chr3:142607799-142607849	NHDF-neo	bronchial:	n/a
48	chr3:142607799-142607849	AG04449	skin:	fetal
49	chr3:142607799-142607849	HEK293	kidney:	embryo
50	chr3:142607799-142607849	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142605846..142608751-chr3:142718093..142722238,5	K562	blood:
2	chr3:73160087..73160608-chr3:142607224..142607863,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAQR9-3	chr3:142607656-142607864	NONHSAT092487

Variant related genes	Relation type
PCOLCE2	TF binding region
PCOLCE2	CpG island
ENSG00000223247	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv437342	chr3:142605233-142622834	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv437343	chr3:142607487-142622834	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142606400-142608200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:142606600-142608600	Active TSS	Right Ventricle	heart
3	chr3:142606600-142609000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:142606800-142608000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr3:142606800-142608200	Active TSS	K562	blood
6	chr3:142606800-142608400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
7	chr3:142606800-142608400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:142606800-142608400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:142606800-142608400	Active TSS	A549	lung
10	chr3:142606800-142608600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr3:142606800-142608600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:142606800-142608800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:142607000-142608000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:142607000-142608000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:142607000-142608000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:142607000-142608000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
17	chr3:142607000-142608200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:142607000-142608200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
20	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
21	chr3:142607000-142608200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
23	chr3:142607000-142608200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:142607000-142608200	Bivalent/Poised TSS	Esophagus	oesophagus
25	chr3:142607000-142608200	Active TSS	Fetal Heart	heart
26	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Thymus	Thymus
27	chr3:142607000-142608400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:142607000-142608400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr3:142607000-142608400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:142607000-142608400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:142607000-142608400	Active TSS	Brain Substantia Nigra	brain
33	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr3:142607000-142608400	Active TSS	Left Ventricle	heart
35	chr3:142607000-142608400	Active TSS	Rectal Smooth Muscle	rectum
36	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
37	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
38	chr3:142607000-142608600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:142607000-142608600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:142607000-142608600	Active TSS	Aorta	Aorta
41	chr3:142607000-142608600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr3:142607000-142608600	Active TSS	Hela-S3	cervix
43	chr3:142607000-142608600	Active TSS	NHLF	lung
44	chr3:142607000-142608800	Active TSS	H9 Cell Line	embryonic stem cell
45	chr3:142607000-142609200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:142607200-142608000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:142607200-142608000	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr3:142607200-142608000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
49	chr3:142607200-142608000	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr3:142607200-142608000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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