Variant report

Variant	rs3738911
Chromosome Location	chr2:113997845-113997846
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	MAX	chr2:113997611-113998199	SK-N-SH	brain:	n/a	n/a
2	SIX5	chr2:113997662-113999126	A549	lung:	n/a	n/a
3	SMARCC1	chr2:113997660-113999427	Hela-S3	cervix:	n/a	chr2:113999386-113999395
4	POLR2A	chr2:113997003-114000128	IMR90	lung:	n/a	n/a
5	FOS	chr2:113997803-113999533	MCF10A-Er-Src	breast:	n/a	chr2:113999384-113999396 chr2:113998584-113998595 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
6	REST	chr2:113997692-113997998	SK-N-SH	brain:	n/a	n/a
7	FOSL2	chr2:113997326-113999659	A549	lung:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113998585-113998596 chr2:113999386-113999394
8	POLR2A	chr2:113996944-114000866	K562	blood:	n/a	n/a
9	SP1	chr2:113997527-113999233	A549	lung:	n/a	n/a
10	POLR2A	chr2:113997427-113998113	ECC-1	luminal epithelium:	n/a	n/a
11	ZNF263	chr2:113997802-113998805	HEK293-T-REx	kidney:	n/a	n/a
12	GATA2	chr2:113997630-113998105	SH-SY5Y	brain:	n/a	n/a
13	POLR2A	chr2:113997475-113999254	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:113997556-113998143	HCT-116	colon:	n/a	n/a
15	MAX	chr2:113997698-113999070	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:113997827-113999157	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr2:113996927-113999829	A549	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
18	FOSL1	chr2:113997636-113999713	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
19	POLR2A	chr2:113997747-113997966	A549	lung:	n/a	n/a
20	SMC3	chr2:113997830-113998030	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr2:113997722-113998154	Hela-S3	cervix:	n/a	n/a
22	RFX5	chr2:113997780-113998126	Hela-S3	cervix:	n/a	n/a
23	GTF2F1	chr2:113997722-113998167	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr2:113997628-113999335	SK-N-SH	brain:	n/a	n/a
25	STAT3	chr2:113997845-113999093	MCF10A-Er-Src	breast:	n/a	n/a
26	TCF12	chr2:113997289-113998206	ECC-1	luminal epithelium:	n/a	n/a
27	MXI1	chr2:113997343-113999336	IMR90	lung:	n/a	n/a
28	POLR2A	chr2:113997740-113998075	HUVEC	blood vessel:	n/a	n/a
29	RAD21	chr2:113997838-113998239	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr2:113997693-113997990	GM12878	blood:	n/a	n/a
31	MYC	chr2:113997694-113999664	MCF10A-Er-Src	breast:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
32	CEBPB	chr2:113997382-113999188	IMR90	lung:	n/a	chr2:113998825-113998836
33	JUND	chr2:113997140-113999306	SK-N-SH	brain:	n/a	chr2:113998584-113998595
34	GATA3	chr2:113997609-113999117	SK-N-SH	brain:	n/a	n/a
35	CEBPB	chr2:113997572-113999797	HCT-116	colon:	n/a	chr2:113998825-113998836
36	NR3C1	chr2:113997620-113998139	A549	lung:	n/a	n/a
37	SIN3AK20	chr2:113997752-113999111	A549	lung:	n/a	n/a
38	POLR2A	chr2:113997705-113998179	A549	lung:	n/a	n/a
39	NFIC	chr2:113997502-113999532	SK-N-SH	brain:	n/a	n/a
40	TCF12	chr2:113997522-113999698	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr2:113997465-113999660	U87	brain:	n/a	n/a
42	STAT3	chr2:113997804-113998196	MCF10A-Er-Src	breast:	n/a	n/a
43	EP300	chr2:113997276-113999114	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr2:113997633-113999727	HCT-116	colon:	n/a	n/a
45	FOSL2	chr2:113997572-113999623	SK-N-SH	brain:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113998585-113998596 chr2:113999386-113999394
46	MXI1	chr2:113997440-113998983	SK-N-SH	brain:	n/a	n/a
47	BHLHE40	chr2:113997725-113998119	K562	blood:	n/a	n/a
48	TFAP2C	chr2:113997756-113998965	Hela-S3	cervix:	n/a	n/a
49	JUND	chr2:113997719-113998277	A549	lung:	n/a	n/a
50	FOSL1	chr2:113997637-113999745	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394

No.	Distal block	Cell Line	Cell type
1	chr2:113952804..113954880-chr2:113996400..113999228,2	MCF-7	breast:
2	chr2:113950220..113951864-chr2:113997428..113999954,2	K562	blood:
3	chr2:113958931..113961853-chr2:113995609..113998129,2	K562	blood:
4	chr17:79828317..79829241-chr2:113997773..113998684,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:113996666-113998402	ENSG00000189223
2	lnc-PSD4-1	chr2:113996666-113998419	NONHSAT073761

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000258395	TF binding region
ENSG00000141522	Chromatin interaction
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2289896	0.89[EUR][1000 genomes]
rs3768767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4322837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58013292	0.89[EUR][1000 genomes]
rs59641602	0.89[EUR][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	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113984000-113998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:113993400-114000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:113994200-114002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:113994600-113998000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:113994600-113998000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:113994600-114000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:113994800-113998000	Weak transcription	Fetal Brain Female	brain
10	chr2:113994800-113998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:113995000-113998200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:113995000-113998800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:113995200-114000000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:113995400-113998000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:113995400-113999000	Enhancers	Fetal Muscle Leg	muscle
19	chr2:113995600-114000200	Weak transcription	Dnd41	blood
20	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
21	chr2:113995800-113999000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr2:113996200-113998200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:113996200-113998800	Genic enhancers	Fetal Kidney	kidney
24	chr2:113996600-114000200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:113996800-113998400	Enhancers	HepG2	liver
26	chr2:113996800-113998600	Enhancers	Fetal Muscle Trunk	muscle
27	chr2:113996800-113999000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr2:113997000-113998000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:113997000-113998000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:113997000-113998000	Genic enhancers	Lung	lung
31	chr2:113997000-113998200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:113997000-113998200	Genic enhancers	Fetal Thymus	thymus
33	chr2:113997000-113998200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr2:113997000-113998200	Enhancers	NHLF	lung
35	chr2:113997000-113998800	Enhancers	Liver	Liver
36	chr2:113997000-113999000	Enhancers	Primary hematopoietic stem cells	blood
37	chr2:113997000-113999000	Enhancers	Fetal Lung	lung
38	chr2:113997000-113999200	Enhancers	Brain Anterior Caudate	brain
39	chr2:113997000-113999200	Enhancers	Brain Cingulate Gyrus	brain
40	chr2:113997000-113999200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:113997000-113999200	Enhancers	Placenta	Placenta
42	chr2:113997000-113999200	Enhancers	Gastric	stomach
43	chr2:113997000-113999200	Enhancers	Right Atrium	heart
44	chr2:113997000-113999200	Genic enhancers	K562	blood
45	chr2:113997000-113999400	Enhancers	Colonic Mucosa	Colon
46	chr2:113997000-113999400	Enhancers	Spleen	Spleen
47	chr2:113997000-113999600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:113997000-113999600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr2:113997000-114000000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:113997000-114000000	Enhancers	Cortex derived primary cultured neurospheres	brain

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