Variant report

Variant	rs540462114
Chromosome Location	chr2:113402258-113402259
allele	C/G
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	NFIC	chr2:113401659-113402422	HepG2	liver:	n/a	n/a
2	HCFC1	chr2:113401734-113404936	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr2:113401815-113402339	HepG2	liver:	n/a	n/a
4	HEY1	chr2:113401600-113404264	HepG2	liver:	n/a	chr2:113403494-113403509 chr2:113403936-113403951 chr2:113403952-113403967 chr2:113403956-113403971 chr2:113403984-113403993
5	POLR2A	chr2:113402006-113404718	IMR90	lung:	n/a	n/a
6	NR2F2	chr2:113401604-113404921	HepG2	liver:	n/a	n/a
7	FOXA1	chr2:113401545-113402419	HepG2	liver:	n/a	n/a
8	FOXA1	chr2:113401647-113402374	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:113401998-113402469	HCT-116	colon:	n/a	n/a
10	FOSL1	chr2:113401751-113403902	HCT-116	colon:	n/a	chr2:113403358-113403367 chr2:113403704-113403712
11	NR2F2	chr2:113401628-113403847	HepG2	liver:	n/a	n/a
12	RFX5	chr2:113401934-113405532	Hela-S3	cervix:	n/a	chr2:113405084-113405099 chr2:113405086-113405103 chr2:113403357-113403366
13	POLR2A	chr2:113401900-113405604	HUVEC	blood vessel:	n/a	n/a
14	MAX	chr2:113402144-113404297	ECC-1	luminal epithelium:	n/a	chr2:113403983-113403993 chr2:113403984-113403993 chr2:113403983-113403994 chr2:113403984-113403994 chr2:113403288-113403298 chr2:113403306-113403315 chr2:113403985-113403992 chr2:113403304-113403319 chr2:113403984-113403993
15	RXRA	chr2:113401707-113402409	HepG2	liver:	n/a	n/a
16	TEAD4	chr2:113401858-113403468	ECC-1	luminal epithelium:	n/a	n/a
17	TCF12	chr2:113401807-113402278	HepG2	liver:	n/a	n/a
18	EP300	chr2:113401905-113403928	HepG2	liver:	n/a	chr2:113403874-113403890 chr2:113403319-113403335 chr2:113403746-113403762
19	TEAD4	chr2:113401899-113402499	HCT-116	colon:	n/a	n/a
20	FOXA1	chr2:113401516-113402376	HepG2	liver:	n/a	n/a
21	HNF4A	chr2:113401759-113402368	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:113401959-113404281	HUVEC	blood vessel:	n/a	n/a
23	ZEB1	chr2:113401479-113402591	HepG2	liver:	n/a	n/a
24	JUND	chr2:113401844-113403910	HCT-116	colon:	n/a	chr2:113403358-113403367 chr2:113403704-113403712 chr2:113402179-113402190
25	MAX	chr2:113402089-113402632	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr2:113401964-113403806	HepG2	liver:	n/a	n/a
27	MYBL2	chr2:113401463-113402396	HepG2	liver:	n/a	n/a
28	FOSL1	chr2:113401763-113402544	HCT-116	colon:	n/a	n/a
29	JUND	chr2:113401928-113402486	Hela-S3	cervix:	n/a	chr2:113402179-113402190
30	UBTF	chr2:113402248-113404684	K562	blood:	n/a	n/a
31	BHLHE40	chr2:113401618-113404082	HepG2	liver:	n/a	chr2:113403746-113403762
32	STAT3	chr2:113402105-113402291	MCF10A-Er-Src	breast:	n/a	n/a
33	MXI1	chr2:113401955-113406269	SK-N-SH	brain:	n/a	chr2:113403307-113403316 chr2:113403983-113403992
34	NR2F2	chr2:113401720-113402555	MCF-7	breast:	n/a	n/a
35	SIN3AK20	chr2:113401891-113402261	A549	lung:	n/a	n/a
36	FOS	chr2:113401934-113402840	MCF10A-Er-Src	breast:	n/a	n/a
37	SMC3	chr2:113401984-113403763	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr2:113401756-113403764	HepG2	liver:	n/a	n/a
39	POLR2A	chr2:113401765-113425023	U87	brain:	n/a	n/a
40	FOS	chr2:113401988-113402377	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr2:113402068-113402430	HepG2	liver:	n/a	n/a
42	TCF7L2	chr2:113401848-113402609	PANC-1	pancreas:	n/a	n/a
43	CHD2	chr2:113402011-113402346	Hela-S3	cervix:	n/a	n/a
44	MAFK	chr2:113401870-113402496	HepG2	liver:	n/a	n/a
45	ZNF263	chr2:113401654-113402846	HEK293-T-REx	kidney:	n/a	n/a
46	HDAC2	chr2:113401658-113402378	HepG2	liver:	n/a	n/a
47	REST	chr2:113401821-113402384	HepG2	liver:	n/a	n/a
48	SP1	chr2:113401680-113403917	HCT-116	colon:	n/a	chr2:113403301-113403310 chr2:113403330-113403342 chr2:113403684-113403696 chr2:113403331-113403341 chr2:113403331-113403341 chr2:113403684-113403696 chr2:113403330-113403342 chr2:113403300-113403311
49	FOS	chr2:113401969-113402698	HUVEC	blood vessel:	n/a	n/a
50	MXI1	chr2:113402005-113404316	IMR90	lung:	n/a	chr2:113403307-113403316 chr2:113403983-113403992

No.	Distal block	Cell Line	Cell type
1	chr2:113385173..113386077-chr2:113402039..113402607,2	Hela-S3	cervix:
2	chr2:112811018..112813475-chr2:113401964..113404333,2	K562	blood:
3	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
4	chr2:113401688..113406035-chr2:113480430..113485744,11	MCF-7	breast:
5	chr2:113399891..113407010-chr2:113481534..113486055,14	K562	blood:
6	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
7	chr2:113400575..113405879-chr2:113475243..113481233,15	K562	blood:
8	chr2:113400910..113403720-chr2:113487016..113489171,3	K562	blood:
9	chr2:113340437..113343949-chr2:113401268..113406617,9	MCF-7	breast:
10	chr2:113298010..113299910-chr2:113402044..113405043,2	MCF-7	breast:
11	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:
12	chr2:113345940..113348650-chr2:113401824..113404479,3	MCF-7	breast:
13	chr2:113297646..113299646-chr2:113402192..113403846,2	K562	blood:
14	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
15	chr2:113339547..113342143-chr2:113401632..113406213,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CKAP2L-1	chr2:113401676-113403267	ENSG00000237753
2	lnc-CKAP2L-1	chr2:113401556-113403368	NONHSAT073714

Variant related genes	Relation type
SLC20A1	TF binding region
ENSG00000231747	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000243389	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000228251	Chromatin interaction
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	esv3335204	chr2:113402081-113405429	Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 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	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
2	chr2:113398400-113402400	Weak transcription	Aorta	Aorta
3	chr2:113398800-113402400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:113398800-113402400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:113398800-113402400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:113399200-113402400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:113399200-113402600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:113399200-113402600	Weak transcription	Lung	lung
9	chr2:113399200-113402600	Weak transcription	Pancreas	Pancrea
10	chr2:113400000-113402400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:113400200-113402400	Enhancers	Fetal Intestine Large	intestine
12	chr2:113400200-113402600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:113400800-113402400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:113401200-113402400	Enhancers	Placenta	Placenta
15	chr2:113401200-113402800	Flanking Active TSS	K562	blood
16	chr2:113401400-113402400	Enhancers	Primary hematopoietic stem cells	blood
17	chr2:113401400-113402400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr2:113401400-113402400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:113401400-113402400	Enhancers	Stomach Mucosa	stomach
20	chr2:113401400-113402400	Flanking Active TSS	HepG2	liver
21	chr2:113401400-113402800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:113401400-113402800	Flanking Active TSS	Osteobl	bone
23	chr2:113401600-113402400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:113401600-113402400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:113401600-113402600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:113401600-113402600	Weak transcription	Small Intestine	intestine
27	chr2:113401600-113402800	Flanking Active TSS	Hela-S3	cervix
28	chr2:113401800-113402400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:113401800-113402600	Flanking Active TSS	A549	lung
30	chr2:113401800-113402800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr2:113401800-113402800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:113401800-113402800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr2:113401800-113402800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:113401800-113402800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr2:113401800-113402800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr2:113401800-113402800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr2:113401800-113402800	Flanking Active TSS	HMEC	breast
38	chr2:113401800-113402800	Flanking Active TSS	NH-A	brain
39	chr2:113401800-113403200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:113402000-113402400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:113402000-113402400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:113402000-113402400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr2:113402000-113402400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:113402000-113402400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr2:113402000-113402400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:113402000-113402400	Enhancers	Brain Substantia Nigra	brain
47	chr2:113402000-113402400	Enhancers	Fetal Brain Male	brain
48	chr2:113402000-113402400	Enhancers	Fetal Muscle Leg	muscle
49	chr2:113402000-113402600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:113402000-113402600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell

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