Variant report

Variant	rs202240420
Chromosome Location	chr3:42644017-42644018
allele	A/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	POLR2A	chr3:42641593-42644059	K562	blood:	n/a	n/a
2	JUND	chr3:42643434-42644100	K562	blood:	n/a	n/a
3	FOS	chr3:42643538-42644039	MCF10A-Er-Src	breast:	n/a	n/a
4	JUND	chr3:42643729-42644064	HepG2	liver:	n/a	n/a
5	CEBPB	chr3:42643705-42644059	ECC-1	luminal epithelium:	n/a	chr3:42643867-42643878
6	STAT3	chr3:42643835-42644063	MCF10A-Er-Src	breast:	n/a	n/a
7	TEAD4	chr3:42641408-42644046	K562	blood:	n/a	n/a
8	STAT3	chr3:42643165-42644091	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr3:42643374-42644033	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr3:42643704-42644108	MCF10A-Er-Src	breast:	n/a	n/a
11	TEAD4	chr3:42643588-42644143	ECC-1	luminal epithelium:	n/a	n/a
12	E2F4	chr3:42643439-42644109	MCF10A-Er-Src	breast:	n/a	n/a
13	ARID3A	chr3:42642770-42644222	K562	blood:	n/a	n/a
14	CEBPB	chr3:42643689-42644108	ECC-1	luminal epithelium:	n/a	chr3:42643867-42643878
15	CEBPB	chr3:42643748-42644032	HepG2	liver:	n/a	chr3:42643867-42643878
16	STAT3	chr3:42643645-42644122	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42604086..42606277-chr3:42642467..42644274,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SS18L2-2	chr3:42642476-42644548	NONHSAT089241

Variant related genes	Relation type
SEC22C	TF binding region
ENSG00000093183	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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv224211	chr3:42644017-42644018	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 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	chr3:42641200-42644200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr3:42641200-42644200	Active TSS	HMEC	breast
3	chr3:42642800-42644200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:42642800-42646200	Weak transcription	Spleen	Spleen
5	chr3:42643000-42644200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:42643000-42644200	Flanking Active TSS	Brain Angular Gyrus	brain
7	chr3:42643000-42644200	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr3:42643000-42644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:42643000-42646200	Weak transcription	Pancreas	Pancrea
10	chr3:42643000-42650000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:42643000-42650000	Weak transcription	Esophagus	oesophagus
12	chr3:42643200-42644200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:42643200-42644200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr3:42643200-42644400	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:42643200-42644600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:42643200-42644800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr3:42643200-42644800	Enhancers	Small Intestine	intestine
18	chr3:42643200-42648400	Weak transcription	Placenta	Placenta
19	chr3:42643200-42649600	Weak transcription	Lung	lung
20	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:42643400-42644200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr3:42643400-42644200	Flanking Active TSS	HUVEC	blood vessel
23	chr3:42643400-42644200	Flanking Active TSS	NH-A	brain
24	chr3:42643400-42647800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:42643600-42644200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:42643600-42644200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:42643600-42644200	Enhancers	Colonic Mucosa	Colon
28	chr3:42643600-42644200	Enhancers	Fetal Heart	heart
29	chr3:42643600-42644200	Enhancers	Fetal Thymus	thymus
30	chr3:42643600-42644200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr3:42643600-42644200	Enhancers	Thymus	Thymus
32	chr3:42643600-42644200	Flanking Active TSS	HepG2	liver
33	chr3:42643600-42644400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:42643600-42644800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:42643600-42644800	Enhancers	Ovary	ovary
36	chr3:42643600-42645600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:42643600-42648400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
39	chr3:42643800-42644200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:42643800-42644200	Enhancers	Primary T cells from cord blood	blood
41	chr3:42643800-42644200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:42643800-42644200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:42643800-42644200	Flanking Active TSS	Fetal Intestine Small	intestine
44	chr3:42643800-42644200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr3:42643800-42644200	Flanking Active TSS	NHLF	lung
46	chr3:42643800-42644400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:42643800-42644400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:42643800-42644800	Enhancers	Gastric	stomach
49	chr3:42643800-42645400	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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