Variant report

Variant	rs562456759
Chromosome Location	chr2:113402506-113402507
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	HCFC1	chr2:113401734-113404936	Hela-S3	cervix:	n/a	n/a
2	HEY1	chr2:113401600-113404264	HepG2	liver:	n/a	chr2:113403494-113403509 chr2:113403936-113403951 chr2:113403952-113403967 chr2:113403956-113403971 chr2:113403984-113403993
3	POLR2A	chr2:113402006-113404718	IMR90	lung:	n/a	n/a
4	NR2F2	chr2:113401604-113404921	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:113402419-113404995	GM12891	blood:	n/a	n/a
6	FOSL1	chr2:113401751-113403902	HCT-116	colon:	n/a	chr2:113403358-113403367 chr2:113403704-113403712
7	NR2F2	chr2:113401628-113403847	HepG2	liver:	n/a	n/a
8	RFX5	chr2:113401934-113405532	Hela-S3	cervix:	n/a	chr2:113405084-113405099 chr2:113405086-113405103 chr2:113403357-113403366
9	POLR2A	chr2:113401900-113405604	HUVEC	blood vessel:	n/a	n/a
10	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
11	CBX3	chr2:113402287-113403745	K562	blood:	n/a	n/a
12	TEAD4	chr2:113401858-113403468	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr2:113401905-113403928	HepG2	liver:	n/a	chr2:113403874-113403890 chr2:113403319-113403335 chr2:113403746-113403762
14	POLR2A	chr2:113401959-113404281	HUVEC	blood vessel:	n/a	n/a
15	ZEB1	chr2:113401479-113402591	HepG2	liver:	n/a	n/a
16	JUND	chr2:113401844-113403910	HCT-116	colon:	n/a	chr2:113403358-113403367 chr2:113403704-113403712 chr2:113402179-113402190
17	MAX	chr2:113402089-113402632	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr2:113401964-113403806	HepG2	liver:	n/a	n/a
19	FOSL1	chr2:113401763-113402544	HCT-116	colon:	n/a	n/a
20	UBTF	chr2:113402248-113404684	K562	blood:	n/a	n/a
21	BHLHE40	chr2:113401618-113404082	HepG2	liver:	n/a	chr2:113403746-113403762
22	KAP1	chr2:113402360-113403531	HEK293	kidney:	n/a	n/a
23	MXI1	chr2:113401955-113406269	SK-N-SH	brain:	n/a	chr2:113403307-113403316 chr2:113403983-113403992
24	NR2F2	chr2:113401720-113402555	MCF-7	breast:	n/a	n/a
25	FOS	chr2:113401934-113402840	MCF10A-Er-Src	breast:	n/a	n/a
26	SMC3	chr2:113401984-113403763	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr2:113401756-113403764	HepG2	liver:	n/a	n/a
28	POLR2A	chr2:113401765-113425023	U87	brain:	n/a	n/a
29	TCF7L2	chr2:113401848-113402609	PANC-1	pancreas:	n/a	n/a
30	FOXM1	chr2:113402484-113403948	GM12878	blood:	n/a	n/a
31	ZNF263	chr2:113401654-113402846	HEK293-T-REx	kidney:	n/a	n/a
32	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
33	RUNX3	chr2:113402392-113404277	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:113402502-113402911	GM12878	blood:	n/a	n/a
35	FOS	chr2:113401969-113402698	HUVEC	blood vessel:	n/a	n/a
36	MXI1	chr2:113402005-113404316	IMR90	lung:	n/a	chr2:113403307-113403316 chr2:113403983-113403992
37	POLR2A	chr2:113401845-113404257	HUVEC	blood vessel:	n/a	n/a
38	TEAD4	chr2:113401900-113402565	HCT-116	colon:	n/a	n/a
39	MAFK	chr2:113401958-113403676	Hela-S3	cervix:	n/a	n/a
40	TCF12	chr2:113401830-113404284	A549	lung:	n/a	n/a
41	TCF7L2	chr2:113401799-113404158	HCT-116	colon:	n/a	n/a
42	POLR2A	chr2:113401707-113407973	U87	brain:	n/a	n/a
43	ARID3A	chr2:113401680-113403636	HepG2	liver:	n/a	n/a
44	JUN	chr2:113401858-113404234	K562	blood:	n/a	chr2:113403358-113403367 chr2:113403704-113403712 chr2:113404177-113404191
45	SP1	chr2:113401721-113403869	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
46	POLR2A	chr2:113401928-113406954	HCT-116	colon:	n/a	n/a
47	POLR2A	chr2:113402016-113412293	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr2:113402480-113402630	NHDF-neo	bronchial:	n/a	n/a
49	MAX	chr2:113402456-113404256	MCF-7	breast:	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
50	JUND	chr2:113402029-113402507	H1-hESC	embryonic stem cell:	n/a	chr2:113402179-113402190

No.	Distal block	Cell Line	Cell type
1	chr2:113339547..113343883-chr2:113402286..113405078,6	K562	blood:
2	chr2:113385173..113386077-chr2:113402039..113402607,2	Hela-S3	cervix:
3	chr2:113298042..113299646-chr2:113402346..113405215,2	K562	blood:
4	chr2:112811018..112813475-chr2:113401964..113404333,2	K562	blood:
5	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
6	chr2:113401688..113406035-chr2:113480430..113485744,11	MCF-7	breast:
7	chr2:113399891..113407010-chr2:113481534..113486055,14	K562	blood:
8	chr2:113031185..113034291-chr2:113402354..113405026,3	K562	blood:
9	chr2:113346825..113348931-chr2:113402265..113404788,2	MCF-7	breast:
10	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
11	chr2:113400575..113405879-chr2:113475243..113481233,15	K562	blood:
12	chr2:113400910..113403720-chr2:113487016..113489171,3	K562	blood:
13	chr2:113340437..113343949-chr2:113401268..113406617,9	MCF-7	breast:
14	chr2:113298010..113299910-chr2:113402044..113405043,2	MCF-7	breast:
15	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:
16	chr2:113345940..113348650-chr2:113401824..113404479,3	MCF-7	breast:
17	chr2:113297646..113299646-chr2:113402192..113403846,2	K562	blood:
18	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
19	chr2:113402414..113404382-chr2:113520815..113523652,2	MCF-7	breast:
20	chr2:113032268..113033936-chr2:113402354..113404096,2	K562	blood:
21	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
3	lnc-CKAP2L-1	chr2:113402475-113403268	NONHSAT073715

Variant related genes	Relation type
SLC20A1	TF binding region
ENSG00000125611	Chromatin interaction
ENSG00000243389	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000169607	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000231747	Chromatin interaction
ENSG00000228251	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv3329842	chr2:113402506-113405054	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 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	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
2	chr2:113399200-113402600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:113399200-113402600	Weak transcription	Lung	lung
4	chr2:113399200-113402600	Weak transcription	Pancreas	Pancrea
5	chr2:113400200-113402600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:113401200-113402800	Flanking Active TSS	K562	blood
7	chr2:113401400-113402800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:113401400-113402800	Flanking Active TSS	Osteobl	bone
9	chr2:113401600-113402600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:113401600-113402600	Weak transcription	Small Intestine	intestine
11	chr2:113401600-113402800	Flanking Active TSS	Hela-S3	cervix
12	chr2:113401800-113402600	Flanking Active TSS	A549	lung
13	chr2:113401800-113402800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:113401800-113402800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:113401800-113402800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr2:113401800-113402800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:113401800-113402800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr2:113401800-113402800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr2:113401800-113402800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr2:113401800-113402800	Flanking Active TSS	HMEC	breast
21	chr2:113401800-113402800	Flanking Active TSS	NH-A	brain
22	chr2:113401800-113403200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:113402000-113402600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:113402000-113402600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
25	chr2:113402000-113402600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr2:113402000-113402600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
27	chr2:113402000-113402600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:113402000-113402600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:113402000-113402600	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr2:113402000-113402600	Flanking Active TSS	Fetal Kidney	kidney
31	chr2:113402000-113402600	Enhancers	Spleen	Spleen
32	chr2:113402000-113402800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:113402000-113402800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
34	chr2:113402000-113402800	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr2:113402000-113402800	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr2:113402000-113402800	Flanking Active TSS	Fetal Heart	heart
37	chr2:113402000-113402800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr2:113402000-113402800	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr2:113402000-113402800	Flanking Active TSS	HSMM	muscle
40	chr2:113402000-113403000	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr2:113402000-113403000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr2:113402000-113403000	Flanking Active TSS	NHEK	skin
43	chr2:113402000-113403200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:113402000-113403200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:113402000-113403200	Flanking Active TSS	HUVEC	blood vessel
46	chr2:113402000-113404800	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr2:113402000-113405000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr2:113402000-113405000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:113402200-113402600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
50	chr2:113402200-113402600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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