Variant report

Variant	rs558020895
Chromosome Location	chr2:113402716-113402717
allele	A/C
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	chr2:113402706-113403914	K562	blood:	n/a	n/a
2	HCFC1	chr2:113401734-113404936	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:113402569-113403760	HepG2	liver:	n/a	n/a
4	TAF1	chr2:113402690-113402911	Hela-S3	cervix:	n/a	n/a
5	YY1	chr2:113402638-113404290	GM12878	blood:	n/a	chr2:113403915-113403929 chr2:113403786-113403800 chr2:113403877-113403891 chr2:113403792-113403801 chr2:113403944-113403955 chr2:113403528-113403542 chr2:113404124-113404135 chr2:113403494-113403505
6	SIN3AK20	chr2:113402628-113404276	PANC-1	pancreas:	n/a	n/a
7	HEY1	chr2:113401600-113404264	HepG2	liver:	n/a	chr2:113403494-113403509 chr2:113403936-113403951 chr2:113403952-113403967 chr2:113403956-113403971 chr2:113403984-113403993
8	POLR2A	chr2:113402006-113404718	IMR90	lung:	n/a	n/a
9	NR2F2	chr2:113401604-113404921	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:113402610-113404242	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr2:113402702-113402891	A549	lung:	n/a	n/a
12	POLR2A	chr2:113402635-113405101	K562	blood:	n/a	n/a
13	POLR2A	chr2:113402659-113402918	A549	lung:	n/a	n/a
14	POLR2A	chr2:113402419-113404995	GM12891	blood:	n/a	n/a
15	RCOR1	chr2:113402708-113403805	GM12878	blood:	n/a	n/a
16	FOSL1	chr2:113401751-113403902	HCT-116	colon:	n/a	chr2:113403358-113403367 chr2:113403704-113403712
17	NR2F2	chr2:113401628-113403847	HepG2	liver:	n/a	n/a
18	HEY1	chr2:113402617-113405042	K562	blood:	n/a	chr2:113403494-113403509 chr2:113403936-113403951 chr2:113403952-113403967 chr2:113403956-113403971 chr2:113403984-113403993
19	RFX5	chr2:113401934-113405532	Hela-S3	cervix:	n/a	chr2:113405084-113405099 chr2:113405086-113405103 chr2:113403357-113403366
20	POLR2A	chr2:113401900-113405604	HUVEC	blood vessel:	n/a	n/a
21	TCF3	chr2:113402654-113404081	GM12878	blood:	n/a	n/a
22	USF1	chr2:113402584-113403723	ECC-1	luminal epithelium:	n/a	n/a
23	BHLHE40	chr2:113402580-113404182	GM12878	blood:	n/a	chr2:113403746-113403762
24	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
25	RELA	chr2:113402665-113403681	GM18951	blood:	n/a	n/a
26	CBX3	chr2:113402287-113403745	K562	blood:	n/a	n/a
27	MAX	chr2:113402680-113403646	Hela-S3	cervix:	n/a	chr2:113403288-113403298 chr2:113403306-113403315 chr2:113403304-113403319
28	NFIC	chr2:113402612-113403724	HepG2	liver:	n/a	n/a
29	MAX	chr2:113402651-113403765	H1-hESC	embryonic stem cell:	n/a	chr2:113403288-113403298 chr2:113403306-113403315 chr2:113403304-113403319
30	MAX	chr2:113402602-113404284	A549	lung:	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
31	TEAD4	chr2:113401858-113403468	ECC-1	luminal epithelium:	n/a	n/a
32	EP300	chr2:113401905-113403928	HepG2	liver:	n/a	chr2:113403874-113403890 chr2:113403319-113403335 chr2:113403746-113403762
33	USF2	chr2:113402588-113403603	K562	blood:	n/a	chr2:113402916-113402927
34	POLR2A	chr2:113402603-113404908	PFSK-1	brain:	n/a	n/a
35	MAFK	chr2:113402634-113402834	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:113402576-113404223	GM12892	blood:	n/a	n/a
37	YY1	chr2:113402615-113403961	SK-N-SH_RA	brain:	n/a	chr2:113403915-113403929 chr2:113403786-113403800 chr2:113403877-113403891 chr2:113403792-113403801 chr2:113403944-113403955 chr2:113403528-113403542 chr2:113403494-113403505
38	MXI1	chr2:113402571-113403905	K562	blood:	n/a	chr2:113403307-113403316
39	CREB1	chr2:113402535-113403771	HepG2	liver:	n/a	n/a
40	POLR2A	chr2:113401959-113404281	HUVEC	blood vessel:	n/a	n/a
41	TCF12	chr2:113402708-113403626	HepG2	liver:	n/a	n/a
42	TAF1	chr2:113402657-113402962	K562	blood:	n/a	n/a
43	HNF4A	chr2:113402698-113403445	HepG2	liver:	n/a	n/a
44	USF1	chr2:113402673-113403730	K562	blood:	n/a	n/a
45	POLR2A	chr2:113402633-113404101	A549	lung:	n/a	n/a
46	HDAC2	chr2:113402570-113403200	MCF-7	breast:	n/a	n/a
47	USF1	chr2:113402669-113403643	HepG2	liver:	n/a	n/a
48	TAF1	chr2:113402700-113404011	K562	blood:	n/a	n/a
49	POLR2A	chr2:113402690-113404507	HepG2	liver:	n/a	n/a
50	USF1	chr2:113402682-113403668	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:113402680-113402730	AG04449	skin:	fetal
2	chr2:113402680-113402730	SK-N-SH_RA	brain:	n/a
3	chr2:113402680-113402730	ovcar-3	ovarian:	n/a
4	chr2:113402680-113402730	SK-N-SH	brain:	n/a
5	chr2:113402680-113402730	HRE	kidney:	n/a
6	chr2:113402680-113402730	T-47D	breast:	n/a
7	chr2:113402680-113402730	AG09319	gingival:	n/a
8	chr2:113402680-113402730	SK-N-MC	brain:	n/a
9	chr2:113402680-113402730	BE2_C	brain:	n/a
10	chr2:113402680-113402730	HRCEpiC	kidney:	n/a
11	chr2:113402680-113402730	Hepatocyte	liver:	n/a
12	chr2:113402680-113402730	HEEpiC	esophagus:	n/a
13	chr2:113402680-113402730	GM12892	blood:	n/a
14	chr2:113402680-113402730	A549	lung:	n/a
15	chr2:113402680-113402730	HPAEpiC	pulmonary alveolar:	n/a
16	chr2:113402680-113402730	HepG2	liver:	n/a
17	chr2:113402680-113402730	NHDF-neo	bronchial:	n/a
18	chr2:113402680-113402730	HNPCEpiC	eye:	n/a
19	chr2:113402680-113402730	NT2-D1	testis:	n/a
20	chr2:113402680-113402730	Jurkat	blood:	n/a
21	chr2:113402680-113402730	HCPEpiC	choroid plexus:	n/a
22	chr2:113402680-113402730	NHBE	bronchial:	n/a
23	chr2:113402680-113402730	BJ	skin:	n/a
24	chr2:113402680-113402730	PrEC	prostate:	n/a
25	chr2:113402680-113402730	PANC-1	pancreas:	n/a
26	chr2:113402680-113402730	NB4	blood:	n/a
27	chr2:113402680-113402730	AG04450	lung:	fetal
28	chr2:113402680-113402730	HRPEpiC	eye:	n/a
29	chr2:113402680-113402730	HIPEpiC	eye:	n/a
30	chr2:113402680-113402730	CMK	blood:	n/a
31	chr2:113402680-113402730	SAEC	small airway:	n/a
32	chr2:113402680-113402730	ProgFib	skin:	n/a
33	chr2:113402680-113402730	K562	blood:	n/a
34	chr2:113402680-113402730	AoSMC	blood vessel:	n/a
35	chr2:113402680-113402730	GM19239	blood:	n/a
36	chr2:113402680-113402730	H1-hESC	embryonic stem cell:	embryo
37	chr2:113402680-113402730	Caco-2	colon:	n/a
38	chr2:113402680-113402730	NH-A	brain:	n/a
39	chr2:113402680-113402730	MCF-7	breast:	n/a
40	chr2:113402680-113402730	RPTEC	kidney:	n/a
41	chr2:113402680-113402730	HL-60	blood:	n/a
42	chr2:113402680-113402730	PFSK-1	brain:	n/a
43	chr2:113402680-113402730	HAEpiC	amniotic membrane:	n/a
44	chr2:113402680-113402730	HMEC	breast:	n/a
45	chr2:113402680-113402730	HCM	heart:	n/a
46	chr2:113402680-113402730	GM12878	blood:	n/a
47	chr2:113402680-113402730	MCF10A-Er-Src	breast:	n/a
48	chr2:113402680-113402730	SKMC	muscle:	n/a
49	chr2:113402680-113402730	ECC-1	luminal epithelium:	n/a
50	chr2:113402680-113402730	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113339547..113343883-chr2:113402286..113405078,6	K562	blood:
2	chr2:113298042..113299646-chr2:113402346..113405215,2	K562	blood:
3	chr2:112811018..112813475-chr2:113401964..113404333,2	K562	blood:
4	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
5	chr2:113401688..113406035-chr2:113480430..113485744,11	MCF-7	breast:
6	chr2:113399891..113407010-chr2:113481534..113486055,14	K562	blood:
7	chr2:113031185..113034291-chr2:113402354..113405026,3	K562	blood:
8	chr2:113346825..113348931-chr2:113402265..113404788,2	MCF-7	breast:
9	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
10	chr2:113400575..113405879-chr2:113475243..113481233,15	K562	blood:
11	chr2:113400910..113403720-chr2:113487016..113489171,3	K562	blood:
12	chr2:113340437..113343949-chr2:113401268..113406617,9	MCF-7	breast:
13	chr2:113298010..113299910-chr2:113402044..113405043,2	MCF-7	breast:
14	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:
15	chr2:113345940..113348650-chr2:113401824..113404479,3	MCF-7	breast:
16	chr2:113297646..113299646-chr2:113402192..113403846,2	K562	blood:
17	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
18	chr2:113402414..113404382-chr2:113520815..113523652,2	MCF-7	breast:
19	chr2:113032268..113033936-chr2:113402354..113404096,2	K562	blood:
20	chr2:113339547..113342143-chr2:113401632..113406213,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CKAP2L-1	chr2:113402609-113402900	XLOC_002275
2	lnc-SLC20A1-1	chr2:113402607-113402992	XLOC_001627
3	lnc-CKAP2L-1	chr2:113401676-113403267	ENSG00000237753
4	lnc-CKAP2L-1	chr2:113401556-113403368	NONHSAT073714
5	lnc-CKAP2L-1	chr2:113402475-113403268	NONHSAT073715

Variant related genes	Relation type
SLC20A1	TF binding region
SLC20A1	CpG island
ENSG00000144130	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000243389	Chromatin interaction
ENSG00000231747	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000228251	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000169607	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113401200-113402800	Flanking Active TSS	K562	blood
2	chr2:113401400-113402800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:113401400-113402800	Flanking Active TSS	Osteobl	bone
4	chr2:113401600-113402800	Flanking Active TSS	Hela-S3	cervix
5	chr2:113401800-113402800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:113401800-113402800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:113401800-113402800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr2:113401800-113402800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:113401800-113402800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:113401800-113402800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr2:113401800-113402800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr2:113401800-113402800	Flanking Active TSS	HMEC	breast
13	chr2:113401800-113402800	Flanking Active TSS	NH-A	brain
14	chr2:113401800-113403200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:113402000-113402800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:113402000-113402800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
17	chr2:113402000-113402800	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr2:113402000-113402800	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr2:113402000-113402800	Flanking Active TSS	Fetal Heart	heart
20	chr2:113402000-113402800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr2:113402000-113402800	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr2:113402000-113402800	Flanking Active TSS	HSMM	muscle
23	chr2:113402000-113403000	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr2:113402000-113403000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr2:113402000-113403000	Flanking Active TSS	NHEK	skin
26	chr2:113402000-113403200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:113402000-113403200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:113402000-113403200	Flanking Active TSS	HUVEC	blood vessel
29	chr2:113402000-113404800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr2:113402000-113405000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr2:113402000-113405000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:113402200-113402800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:113402200-113402800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:113402200-113402800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr2:113402200-113402800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:113402200-113402800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:113402200-113402800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr2:113402200-113402800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:113402200-113402800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:113402200-113402800	Flanking Active TSS	Liver	Liver
41	chr2:113402200-113402800	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr2:113402200-113402800	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr2:113402200-113402800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr2:113402200-113402800	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr2:113402200-113402800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:113402200-113402800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr2:113402200-113402800	Active TSS	Right Atrium	heart
48	chr2:113402200-113402800	Flanking Active TSS	Dnd41	blood
49	chr2:113402200-113402800	Flanking Active TSS	GM12878-XiMat	blood
50	chr2:113402200-113402800	Flanking Active TSS	HSMMtube	muscle

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