Variant report

Variant	rs368648610
Chromosome Location	chr3:142607702-142607703
allele	G/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	MAX	chr3:142606853-142608072	Hela-S3	cervix:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
11	CTBP2	chr3:142607012-142608279	H1-hESC	embryonic stem cell:	n/a	n/a
12	E2F6	chr3:142606856-142608302	H1-hESC	embryonic stem cell:	n/a	chr3:142608047-142608057
13	E2F1	chr3:142607199-142608071	Hela-S3	cervix:	n/a	chr3:142607723-142607734 chr3:142608047-142608057
14	SMARCB1	chr3:142607002-142608275	Hela-S3	cervix:	n/a	n/a
15	MYC	chr3:142607241-142607858	MCF-7	breast:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
16	CTCF	chr3:142607695-142607717	MCF-7	breast:	n/a	n/a
17	JUND	chr3:142607095-142607943	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:142606943-142608096	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr3:142606972-142607916	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:142607029-142608091	H1-hESC	embryonic stem cell:	n/a	n/a
21	TBP	chr3:142606978-142608376	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:142607610-142607902	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:142607644-142608092	ProgFib	skin:	n/a	n/a
24	ZBTB7A	chr3:142607469-142608248	K562	blood:	n/a	chr3:142607642-142607651
25	CHD2	chr3:142607358-142607738	HepG2	liver:	n/a	n/a
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	MAX	chr3:142606830-142608243	A549	lung:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
34	RCOR1	chr3:142607644-142607990	HepG2	liver:	n/a	n/a
35	E2F6	chr3:142606919-142608092	H1-hESC	embryonic stem cell:	n/a	chr3:142608047-142608057
36	YY1	chr3:142607554-142608104	ECC-1	luminal epithelium:	n/a	n/a
37	MYC	chr3:142607132-142607870	K562	blood:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
38	POLR2A	chr3:142607319-142608120	A549	lung:	n/a	n/a
39	CREB1	chr3:142607682-142608148	A549	lung:	n/a	n/a
40	SMC3	chr3:142606932-142608036	Hela-S3	cervix:	n/a	chr3:142607390-142607404
41	SIN3A	chr3:142606970-142608279	H1-hESC	embryonic stem cell:	n/a	chr3:142607930-142607941 chr3:142607169-142607178
42	POLR2A	chr3:142607482-142608015	MCF-7	breast:	n/a	n/a
43	TAF1	chr3:142606915-142608073	A549	lung:	n/a	n/a
44	MYC	chr3:142607157-142607835	H1-hESC	embryonic stem cell:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
45	POLR2A	chr3:142606945-142608129	HCT-116	colon:	n/a	n/a
46	HA-E2F1	chr3:142607158-142608147	Hela-S3	cervix:	n/a	chr3:142607723-142607734 chr3:142608047-142608057
47	POLR2A	chr3:142606975-142608191	HEK293	kidney:	n/a	n/a
48	ZKSCAN1	chr3:142607070-142607963	Hela-S3	cervix:	n/a	n/a
49	MAX	chr3:142606906-142608064	H1-hESC	embryonic stem cell:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
50	POLR2A	chr3:142606987-142608175	H1-hESC	embryonic stem cell:	n/a	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
2	lnc-PAQR9-3	chr3:142607656-142607769	NONHSAT092489

Variant related genes	Relation type
PCOLCE2	TF binding region
ENSG00000163714	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000223247	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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142606000-142607800	Active TSS	Right Atrium	heart
2	chr3:142606400-142608200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:142606600-142608600	Active TSS	Right Ventricle	heart
4	chr3:142606600-142609000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:142606800-142608000	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr3:142606800-142608200	Active TSS	K562	blood
7	chr3:142606800-142608400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
8	chr3:142606800-142608400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:142606800-142608400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:142606800-142608400	Active TSS	A549	lung
11	chr3:142606800-142608600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr3:142606800-142608600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:142606800-142608800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:142607000-142607800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
15	chr3:142607000-142607800	Flanking Active TSS	Liver	Liver
16	chr3:142607000-142607800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
17	chr3:142607000-142607800	Flanking Bivalent TSS/Enh	HepG2	liver
18	chr3:142607000-142607800	Flanking Active TSS	HMEC	breast
19	chr3:142607000-142608000	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr3:142607000-142608000	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr3:142607000-142608000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr3:142607000-142608000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
23	chr3:142607000-142608200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:142607000-142608200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
26	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
27	chr3:142607000-142608200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
29	chr3:142607000-142608200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:142607000-142608200	Bivalent/Poised TSS	Esophagus	oesophagus
31	chr3:142607000-142608200	Active TSS	Fetal Heart	heart
32	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Thymus	Thymus
33	chr3:142607000-142608400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:142607000-142608400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
35	chr3:142607000-142608400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:142607000-142608400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:142607000-142608400	Active TSS	Brain Substantia Nigra	brain
39	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr3:142607000-142608400	Active TSS	Left Ventricle	heart
41	chr3:142607000-142608400	Active TSS	Rectal Smooth Muscle	rectum
42	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
43	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr3:142607000-142608600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:142607000-142608600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:142607000-142608600	Active TSS	Aorta	Aorta
47	chr3:142607000-142608600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
48	chr3:142607000-142608600	Active TSS	Hela-S3	cervix
49	chr3:142607000-142608600	Active TSS	NHLF	lung
50	chr3:142607000-142608800	Active TSS	H9 Cell Line	embryonic stem cell

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