Variant report

Variant	rs2196900
Chromosome Location	chr3:142608087-142608088
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	CTCF	chr3:142608000-142608150	SK-N-SH_RA	brain:	n/a	chr3:142608047-142608060 chr3:142608082-142608095
2	MAX	chr3:142606829-142608177	HCT-116	colon:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
3	MAX	chr3:142607125-142608144	SK-N-SH	brain:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
4	MAX	chr3:142606806-142608167	ECC-1	luminal epithelium:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
5	TCF7L2	chr3:142607030-142608204	HCT-116	colon:	n/a	n/a
6	CTBP2	chr3:142607012-142608279	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr3:142606856-142608302	H1-hESC	embryonic stem cell:	n/a	chr3:142608047-142608057
8	SMARCB1	chr3:142607002-142608275	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr3:142608060-142608210	AG04449	skin:	n/a	chr3:142608082-142608095
10	POLR2A	chr3:142606943-142608096	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:142607029-142608091	H1-hESC	embryonic stem cell:	n/a	n/a
12	TBP	chr3:142606978-142608376	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:142607644-142608092	ProgFib	skin:	n/a	n/a
14	ZBTB7A	chr3:142607469-142608248	K562	blood:	n/a	chr3:142607642-142607651
15	TAF1	chr3:142607008-142608169	H1-hESC	embryonic stem cell:	n/a	n/a
16	TCF7L2	chr3:142607888-142608146	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:142606946-142608115	Hela-S3	cervix:	n/a	n/a
18	MYC	chr3:142606855-142608204	A549	lung:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
19	MAX	chr3:142606984-142608208	NB4	blood:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
20	E2F6	chr3:142607114-142608109	K562	blood:	n/a	chr3:142608047-142608057
21	MAX	chr3:142606830-142608243	A549	lung:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
22	E2F6	chr3:142606919-142608092	H1-hESC	embryonic stem cell:	n/a	chr3:142608047-142608057
23	YY1	chr3:142607554-142608104	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr3:142607319-142608120	A549	lung:	n/a	n/a
25	CREB1	chr3:142607682-142608148	A549	lung:	n/a	n/a
26	SIN3A	chr3:142606970-142608279	H1-hESC	embryonic stem cell:	n/a	chr3:142607930-142607941 chr3:142607169-142607178
27	POLR2A	chr3:142606945-142608129	HCT-116	colon:	n/a	n/a
28	HA-E2F1	chr3:142607158-142608147	Hela-S3	cervix:	n/a	chr3:142607723-142607734 chr3:142608047-142608057
29	POLR2A	chr3:142606975-142608191	HEK293	kidney:	n/a	n/a
30	POLR2A	chr3:142606987-142608175	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr3:142606939-142608158	H1-hESC	embryonic stem cell:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
32	HMGN3	chr3:142607302-142608265	K562	blood:	n/a	n/a
33	CTCF	chr3:142607940-142608090	HCPEpiC	choroid plexus:	n/a	chr3:142608047-142608060
34	POLR2A	chr3:142607302-142608106	H1-neurons	neurons:	n/a	n/a
35	MAX	chr3:142606870-142608106	MCF-7	breast:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
36	REST	chr3:142606983-142608227	H1-neurons	neurons:	n/a	chr3:142607169-142607179 chr3:142608061-142608081
37	MAX	chr3:142606765-142608275	A549	lung:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
38	SMARCC1	chr3:142607081-142608198	Hela-S3	cervix:	n/a	n/a
39	MXI1	chr3:142606690-142608500	SK-N-SH	brain:	n/a	chr3:142607393-142607402 chr3:142607391-142607400
40	MAX	chr3:142606881-142608147	Hela-S3	cervix:	n/a	chr3:142607392-142607401 chr3:142607392-142607401 chr3:142607391-142607401 chr3:142607392-142607401
41	TCF7L2	chr3:142607531-142608163	PANC-1	pancreas:	n/a	n/a
42	CCNT2	chr3:142607960-142608143	K562	blood:	n/a	n/a
43	UBTF	chr3:142607833-142608122	K562	blood:	n/a	n/a
44	POLR2A	chr3:142606752-142608314	H1-hESC	embryonic stem cell:	n/a	n/a
45	HA-E2F1	chr3:142606964-142608205	MCF-7	breast:	n/a	chr3:142607723-142607734 chr3:142608047-142608057
46	E2F6	chr3:142606832-142608269	A549	lung:	n/a	chr3:142608047-142608057
47	POLR2A	chr3:142607307-142608127	A549	lung:	n/a	n/a
48	POLR2A	chr3:142606967-142608243	H1-hESC	embryonic stem cell:	n/a	n/a
49	ZBTB7A	chr3:142607461-142608253	ECC-1	luminal epithelium:	n/a	chr3:142607642-142607651
50	BACH1	chr3:142607083-142608248	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142608037-142608087	SK-N-SH_RA	brain:	n/a
2	chr3:142608051-142608101	AoSMC	blood vessel:	n/a
3	chr3:142608037-142608087	HPAEpiC	pulmonary alveolar:	n/a
4	chr3:142608037-142608087	U87	brain:	n/a
5	chr3:142608063-142608113	NHDF-neo	bronchial:	n/a
6	chr3:142608063-142608113	GM12878	blood:	n/a
7	chr3:142608063-142608113	HCF	heart:	n/a
8	chr3:142608037-142608087	HIPEpiC	eye:	n/a
9	chr3:142608063-142608113	HAEpiC	amniotic membrane:	n/a
10	chr3:142608063-142608113	HCPEpiC	choroid plexus:	n/a
11	chr3:142608063-142608113	RPTEC	kidney:	n/a
12	chr3:142608051-142608101	HCF	heart:	n/a
13	chr3:142608037-142608087	HRE	kidney:	n/a
14	chr3:142608063-142608113	SK-N-SH_RA	brain:	n/a
15	chr3:142608037-142608087	Hela-S3	cervix:	n/a
16	chr3:142608051-142608101	HCPEpiC	choroid plexus:	n/a
17	chr3:142608037-142608087	GM19239	blood:	n/a
18	chr3:142608063-142608113	GM19239	blood:	n/a
19	chr3:142608063-142608113	K562	blood:	n/a
20	chr3:142608051-142608101	AG04449	skin:	fetal
21	chr3:142608051-142608101	Caco-2	colon:	n/a
22	chr3:142608037-142608087	AG10803	skin:	n/a
23	chr3:142608063-142608113	NB4	blood:	n/a
24	chr3:142608063-142608113	LNCaP	prostate:	n/a
25	chr3:142608037-142608087	PFSK-1	brain:	n/a
26	chr3:142608037-142608087	SAEC	small airway:	n/a
27	chr3:142608037-142608087	HUVEC	blood vessel:	n/a
28	chr3:142608063-142608113	HCM	heart:	n/a
29	chr3:142608051-142608101	HMEC	breast:	n/a
30	chr3:142608037-142608087	HRCEpiC	kidney:	n/a
31	chr3:142608037-142608087	HCF	heart:	n/a
32	chr3:142608037-142608087	AG04450	lung:	fetal
33	chr3:142608037-142608087	Hepatocyte	liver:	n/a
34	chr3:142608063-142608113	ovcar-3	ovarian:	n/a
35	chr3:142608037-142608087	NB4	blood:	n/a
36	chr3:142608063-142608113	A549	lung:	n/a
37	chr3:142608063-142608113	SK-N-SH	brain:	n/a
38	chr3:142608051-142608101	HRE	kidney:	n/a
39	chr3:142608051-142608101	HIPEpiC	eye:	n/a
40	chr3:142608063-142608113	H1-hESC	embryonic stem cell:	embryo
41	chr3:142608063-142608113	MCF-7	breast:	n/a
42	chr3:142608037-142608087	LNCaP	prostate:	n/a
43	chr3:142608051-142608101	BJ	skin:	n/a
44	chr3:142608051-142608101	Jurkat	blood:	n/a
45	chr3:142608037-142608087	HepG2	liver:	n/a
46	chr3:142608051-142608101	K562	blood:	n/a
47	chr3:142608051-142608101	A549	lung:	n/a
48	chr3:142608051-142608101	ECC-1	luminal epithelium:	n/a
49	chr3:142608063-142608113	HEK293	kidney:	embryo
50	chr3:142608037-142608087	PrEC	prostate:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142605846..142608751-chr3:142718093..142722238,5	K562	blood:

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

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2248811	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581624	0.82[AMR][1000 genomes]
rs2581634	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59716354	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6778966	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:122 , 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	chr3:142606800-142608200	Active TSS	K562	blood
5	chr3:142606800-142608400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr3:142606800-142608400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:142606800-142608400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:142606800-142608400	Active TSS	A549	lung
9	chr3:142606800-142608600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr3:142606800-142608600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:142606800-142608800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:142607000-142608200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:142607000-142608200	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
15	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
16	chr3:142607000-142608200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
18	chr3:142607000-142608200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:142607000-142608200	Bivalent/Poised TSS	Esophagus	oesophagus
20	chr3:142607000-142608200	Active TSS	Fetal Heart	heart
21	chr3:142607000-142608200	Flanking Bivalent TSS/Enh	Thymus	Thymus
22	chr3:142607000-142608400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:142607000-142608400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr3:142607000-142608400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:142607000-142608400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:142607000-142608400	Active TSS	Brain Substantia Nigra	brain
28	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr3:142607000-142608400	Active TSS	Left Ventricle	heart
30	chr3:142607000-142608400	Active TSS	Rectal Smooth Muscle	rectum
31	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
32	chr3:142607000-142608400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr3:142607000-142608600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:142607000-142608600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:142607000-142608600	Active TSS	Aorta	Aorta
36	chr3:142607000-142608600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:142607000-142608600	Active TSS	Hela-S3	cervix
38	chr3:142607000-142608600	Active TSS	NHLF	lung
39	chr3:142607000-142608800	Active TSS	H9 Cell Line	embryonic stem cell
40	chr3:142607000-142609200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:142607200-142608200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
42	chr3:142607200-142608200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:142607200-142608200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:142607200-142608200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
45	chr3:142607200-142608200	Active TSS	NHDF-Ad	bronchial
46	chr3:142607200-142608400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:142607200-142608400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:142607200-142608600	Active TSS	Brain Cingulate Gyrus	brain
49	chr3:142607200-142608600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
50	chr3:142607200-142608600	Active TSS	Pancreatic Islets	Pancreatic Islet

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