Variant report

Variant	rs2240985
Chromosome Location	chr2:37899654-37899655
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	SIN3AK20	chr2:37897957-37900316	HCT-116	colon:	n/a	n/a
2	POU2F2	chr2:37899610-37900061	GM12878	blood:	n/a	chr2:37899859-37899871 chr2:37899734-37899745
3	POLR2A	chr2:37898485-37900160	HCT-116	colon:	n/a	n/a
4	ZMIZ1	chr2:37899370-37899659	K562	blood:	n/a	n/a
5	STAT5A	chr2:37897890-37900133	GM12878	blood:	n/a	chr2:37898870-37898882
6	POLR2A	chr2:37898298-37900041	A549	lung:	n/a	n/a
7	RUNX3	chr2:37899038-37900258	GM12878	blood:	n/a	n/a
8	MAX	chr2:37898958-37899694	MCF-7	breast:	n/a	n/a
9	NR2F2	chr2:37899104-37900294	MCF-7	breast:	n/a	n/a
10	GABPA	chr2:37899033-37900046	A549	lung:	n/a	chr2:37899159-37899168
11	RAD21	chr2:37897973-37900206	SK-N-SH_RA	brain:	n/a	chr2:37898586-37898600 chr2:37898603-37898617 chr2:37899859-37899869 chr2:37898132-37898144
12	NR3C1	chr2:37899646-37900182	A549	lung:	n/a	n/a
13	STAT1	chr2:37899196-37900174	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:37898053-37900165	GM19193	blood:	n/a	n/a
15	POLR2A	chr2:37898081-37899933	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr2:37899179-37900271	K562	blood:	n/a	n/a
17	RELA	chr2:37899182-37900086	GM18951	blood:	n/a	n/a
18	JUND	chr2:37899653-37900135	A549	lung:	n/a	n/a
19	TBP	chr2:37899164-37900141	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr2:37899460-37899690	Caco-2	colon:	n/a	n/a
21	ZEB1	chr2:37899283-37899903	GM12878	blood:	n/a	n/a
22	EBF1	chr2:37899219-37900114	GM12878	blood:	n/a	n/a
23	RELA	chr2:37898108-37900253	GM12891	blood:	n/a	n/a
24	ZBTB7A	chr2:37898181-37900278	ECC-1	luminal epithelium:	n/a	chr2:37899331-37899342
25	FOSL2	chr2:37899050-37900216	A549	lung:	n/a	chr2:37899399-37899413
26	MAZ	chr2:37898229-37900318	K562	blood:	n/a	chr2:37898755-37898765 chr2:37898880-37898890
27	POLR2A	chr2:37897924-37900222	GM12892	blood:	n/a	n/a
28	POLR2A	chr2:37898362-37900073	ECC-1	luminal epithelium:	n/a	n/a
29	SIN3AK20	chr2:37897864-37900261	SK-N-SH	brain:	n/a	n/a
30	YY1	chr2:37898380-37900110	GM12892	blood:	n/a	chr2:37898877-37898891 chr2:37898886-37898900 chr2:37898550-37898561 chr2:37898706-37898720 chr2:37899015-37899026 chr2:37899274-37899288
31	POLR2A	chr2:37898376-37900069	HUVEC	blood vessel:	n/a	n/a
32	RAD21	chr2:37896163-37900083	IMR90	lung:	n/a	chr2:37896743-37896757 chr2:37898586-37898600 chr2:37898603-37898617 chr2:37899859-37899869 chr2:37896892-37896906 chr2:37898132-37898144
33	POLR2A	chr2:37897952-37900213	GM12878	blood:	n/a	n/a
34	E2F6	chr2:37899196-37900205	H1-hESC	embryonic stem cell:	n/a	chr2:37899335-37899350
35	POLR2A	chr2:37898135-37899979	GM10847	blood:	n/a	n/a
36	CTBP2	chr2:37897986-37900111	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr2:37899164-37899839	MCF-7	breast:	n/a	n/a
38	CTCF	chr2:37899580-37899730	GM12873	blood:	n/a	n/a
39	MYC	chr2:37898628-37900067	A549	lung:	n/a	chr2:37898755-37898765 chr2:37898880-37898890
40	BCL3	chr2:37898882-37900267	A549	lung:	n/a	chr2:37899281-37899290 chr2:37899337-37899346 chr2:37898885-37898898
41	TAF1	chr2:37899172-37899730	GM12878	blood:	n/a	n/a
42	GABPA	chr2:37899179-37900156	SK-N-SH	brain:	n/a	n/a
43	ZBTB7A	chr2:37899577-37900056	K562	blood:	n/a	n/a
44	SP1	chr2:37899172-37899683	H1-hESC	embryonic stem cell:	n/a	n/a
45	GATA3	chr2:37899654-37900080	T-47D	breast:	n/a	chr2:37899808-37899818
46	POLR2A	chr2:37898849-37899711	HL-60	blood:	n/a	n/a
47	NFATC1	chr2:37899610-37900133	GM12878	blood:	n/a	n/a
48	POLR2A	chr2:37899636-37900255	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr2:37898185-37899736	GM12891	blood:	n/a	n/a
50	MYC	chr2:37899254-37899947	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37897976..37899851-chr2:37913464..37916015,2	MCF-7	breast:
2	chr2:37899209..37899972-chr4:125633775..125634624,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM82A1-11	chr2:37898911-37899815	NONHSAT070135
2	lnc-FAM82A1-11	chr2:37899328-37900292	NONHSAT070136

Variant related genes	Relation type
CDC42EP3	TF binding region
ENSG00000163171	Chromatin interaction
ENSG00000151458	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11124597	0.88[ASN][1000 genomes]
rs12615921	0.87[ASN][1000 genomes]
rs17523989	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670750	0.85[ASN][1000 genomes]
rs4670751	0.84[ASN][1000 genomes]
rs4670758	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4670760	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59984376	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61233180	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs729793	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309014	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv998567	chr2:37886244-37910627	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37894600-37900200	Active TSS	Right Atrium	heart
2	chr2:37894600-37900200	Active TSS	Right Ventricle	heart
3	chr2:37894800-37900200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:37894800-37900400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr2:37895000-37900200	Active TSS	Psoas Muscle	Psoas
6	chr2:37895200-37900400	Active TSS	Aorta	Aorta
7	chr2:37895400-37899800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:37895600-37900200	Active TSS	Brain Angular Gyrus	brain
9	chr2:37895600-37900200	Active TSS	Fetal Kidney	kidney
10	chr2:37895600-37900400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:37895800-37900200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:37895800-37900200	Active TSS	Left Ventricle	heart
13	chr2:37896000-37899800	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:37896000-37899800	Active TSS	NHLF	lung
15	chr2:37896000-37900200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:37896200-37899800	Active TSS	Primary monocytes fromperipheralblood	blood
17	chr2:37896200-37900000	Active TSS	Monocytes-CD14+_RO01746	blood
18	chr2:37896200-37900200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:37896200-37900200	Active TSS	Colon Smooth Muscle	Colon
20	chr2:37896200-37900400	Active TSS	GM12878-XiMat	blood
21	chr2:37896400-37900000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:37896400-37900200	Active TSS	Lung	lung
23	chr2:37896600-37900400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:37896800-37899800	Active TSS	HMEC	breast
25	chr2:37896800-37900000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:37896800-37900000	Active TSS	Fetal Heart	heart
27	chr2:37896800-37900400	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:37896800-37900400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr2:37896800-37900400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:37897000-37900000	Active TSS	Ovary	ovary
31	chr2:37897000-37900200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:37897200-37900000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:37897200-37900200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr2:37897200-37900200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr2:37897200-37900400	Active TSS	H1 Cell Line	embryonic stem cell
36	chr2:37897400-37899800	Active TSS	Gastric	stomach
37	chr2:37897400-37900000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:37897400-37900000	Active TSS	Small Intestine	intestine
39	chr2:37897400-37900200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:37897400-37900200	Active TSS	Pancreas	Pancrea
41	chr2:37897400-37900400	Active TSS	Fetal Brain Female	brain
42	chr2:37897600-37899800	Active TSS	HUVEC	blood vessel
43	chr2:37897600-37900000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:37897600-37900000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:37897600-37900000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:37897600-37900000	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr2:37897600-37900000	Active TSS	A549	lung
48	chr2:37897600-37900000	Active TSS	HSMM	muscle
49	chr2:37897600-37900200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:37897600-37900400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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