Variant report

Variant	rs542255673
Chromosome Location	chr2:97426603-97426604
allele	A/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	MAX	chr2:97425868-97427547	A549	lung:	n/a	chr2:97426333-97426340 chr2:97426332-97426341
2	POLR2A	chr2:97426165-97427172	GM12892	blood:	n/a	n/a
3	IRF1	chr2:97426293-97426952	K562	blood:	n/a	chr2:97426547-97426561
4	MAX	chr2:97425916-97427312	HCT-116	colon:	n/a	chr2:97426333-97426340 chr2:97426332-97426341
5	POLR2A	chr2:97426182-97426914	U87	brain:	n/a	n/a
6	EGR1	chr2:97426229-97426918	K562	blood:	n/a	chr2:97426548-97426558 chr2:97426435-97426448 chr2:97426544-97426558 chr2:97426575-97426589 chr2:97426543-97426556
7	RAD21	chr2:97426253-97426996	IMR90	lung:	n/a	n/a
8	SP1	chr2:97426186-97426741	A549	lung:	n/a	chr2:97426549-97426558 chr2:97426548-97426558 chr2:97426548-97426557 chr2:97426548-97426558 chr2:97426547-97426559 chr2:97426547-97426559 chr2:97426549-97426558
9	EP300	chr2:97426202-97426806	K562	blood:	n/a	chr2:97426235-97426249
10	JUND	chr2:97426210-97426916	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr2:97425965-97427284	ECC-1	luminal epithelium:	n/a	chr2:97426333-97426340 chr2:97426332-97426341
12	MYC	chr2:97426196-97426852	MCF10A-Er-Src	breast:	n/a	chr2:97426333-97426340 chr2:97426332-97426341
13	MAX	chr2:97426046-97426656	H1-hESC	embryonic stem cell:	n/a	chr2:97426333-97426340 chr2:97426332-97426341
14	FOXP2	chr2:97426261-97427235	PFSK-1	brain:	n/a	n/a
15	MAX	chr2:97425953-97426762	ECC-1	luminal epithelium:	n/a	chr2:97426333-97426340 chr2:97426332-97426341
16	CTCF	chr2:97426601-97426954	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:97426238-97426963	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr2:97425978-97426848	PFSK-1	brain:	n/a	n/a
19	RCOR1	chr2:97426112-97426992	Hela-S3	cervix:	n/a	n/a
20	MAX	chr2:97426140-97427123	NB4	blood:	n/a	chr2:97426333-97426340 chr2:97426332-97426341
21	CTCF	chr2:97426566-97427003	A549	lung:	n/a	n/a
22	RCOR1	chr2:97426037-97427339	K562	blood:	n/a	n/a
23	POLR2A	chr2:97426132-97427020	HUVEC	blood vessel:	n/a	n/a
24	SMC3	chr2:97426365-97427091	K562	blood:	n/a	n/a
25	POLR2A	chr2:97426093-97427137	Hela-S3	cervix:	n/a	n/a
26	ZMIZ1	chr2:97426029-97426985	K562	blood:	n/a	n/a
27	POU2F2	chr2:97426573-97426774	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:97425902-97427318	MCF10A-Er-Src	breast:	n/a	n/a
29	EGR1	chr2:97426194-97426983	K562	blood:	n/a	chr2:97426548-97426558 chr2:97426435-97426448 chr2:97426544-97426558 chr2:97426575-97426589 chr2:97426543-97426556
30	POLR2A	chr2:97426211-97426862	HCT-116	colon:	n/a	n/a
31	RAD21	chr2:97426275-97426973	SK-N-SH_RA	brain:	n/a	n/a
32	WRNIP1	chr2:97426107-97426631	GM12878	blood:	n/a	n/a
33	TAF1	chr2:97426239-97426915	ECC-1	luminal epithelium:	n/a	n/a
34	RAD21	chr2:97426602-97426934	GM12878	blood:	n/a	n/a
35	ZNF143	chr2:97426224-97427382	GM12878	blood:	n/a	n/a
36	PML	chr2:97426591-97426765	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:97426246-97427223	MCF-7	breast:	n/a	n/a
38	MAZ	chr2:97426266-97427135	HepG2	liver:	n/a	chr2:97426333-97426340 chr2:97426332-97426341
39	EGR1	chr2:97426093-97426969	MCF-7	breast:	n/a	chr2:97426548-97426558 chr2:97426435-97426448 chr2:97426544-97426558 chr2:97426575-97426589 chr2:97426543-97426556
40	CHD2	chr2:97426281-97427067	HepG2	liver:	n/a	n/a
41	HEY1	chr2:97426469-97426875	K562	blood:	n/a	chr2:97426478-97426493 chr2:97426543-97426558
42	HEY1	chr2:97426222-97426986	HepG2	liver:	n/a	chr2:97426478-97426493 chr2:97426543-97426558
43	CTCF	chr2:97426270-97427079	GM12878	blood:	n/a	n/a
44	BCL3	chr2:97426561-97426955	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:97426238-97426862	GM12891	blood:	n/a	n/a
46	POLR2A	chr2:97426231-97427170	HepG2	liver:	n/a	n/a
47	HCFC1	chr2:97426308-97427358	K562	blood:	n/a	n/a
48	HEY1	chr2:97426214-97426859	K562	blood:	n/a	chr2:97426478-97426493 chr2:97426543-97426558
49	POLR2A	chr2:97426210-97427025	A549	lung:	n/a	n/a
50	MAX	chr2:97426114-97427215	A549	lung:	n/a	chr2:97426333-97426340 chr2:97426332-97426341

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:97426602-97426652	HL-60	blood:	n/a
2	chr2:97426598-97426648	H1-hESC	embryonic stem cell:	embryo
3	chr2:97426602-97426652	HCM	heart:	n/a
4	chr2:97426602-97426652	HEK293	kidney:	embryo
5	chr2:97426602-97426652	BE2_C	brain:	n/a
6	chr2:97426602-97426652	T-47D	breast:	n/a
7	chr2:97426598-97426648	Caco-2	colon:	n/a
8	chr2:97426602-97426652	NB4	blood:	n/a
9	chr2:97426602-97426652	Hepatocyte	liver:	n/a
10	chr2:97426598-97426648	AG10803	skin:	n/a
11	chr2:97426602-97426652	AG09319	gingival:	n/a
12	chr2:97426602-97426652	NT2-D1	testis:	n/a
13	chr2:97426602-97426652	H1-hESC	embryonic stem cell:	embryo
14	chr2:97426602-97426652	HMEC	breast:	n/a
15	chr2:97426598-97426648	PFSK-1	brain:	n/a
16	chr2:97426602-97426652	U87	brain:	n/a
17	chr2:97426602-97426652	GM06990	blood:	n/a
18	chr2:97426602-97426652	PrEC	prostate:	n/a
19	chr2:97426598-97426648	NH-A	brain:	n/a
20	chr2:97426602-97426652	K562	blood:	n/a
21	chr2:97426602-97426652	PANC-1	pancreas:	n/a
22	chr2:97426602-97426652	ECC-1	luminal epithelium:	n/a
23	chr2:97426602-97426652	CMK	blood:	n/a
24	chr2:97426598-97426648	T-47D	breast:	n/a
25	chr2:97426598-97426648	HCM	heart:	n/a
26	chr2:97426598-97426648	ECC-1	luminal epithelium:	n/a
27	chr2:97426598-97426648	MCF-7	breast:	n/a
28	chr2:97426598-97426648	GM06990	blood:	n/a
29	chr2:97426602-97426652	GM12892	blood:	n/a
30	chr2:97426598-97426648	HCT-116	colon:	n/a
31	chr2:97426602-97426652	NH-A	brain:	n/a
32	chr2:97426602-97426652	HPAEpiC	pulmonary alveolar:	n/a
33	chr2:97426598-97426648	U87	brain:	n/a
34	chr2:97426602-97426652	NHDF-neo	bronchial:	n/a
35	chr2:97426602-97426652	PFSK-1	brain:	n/a
36	chr2:97426602-97426652	SK-N-SH_RA	brain:	n/a
37	chr2:97426598-97426648	HCF	heart:	n/a
38	chr2:97426598-97426648	HEK293	kidney:	embryo
39	chr2:97426598-97426648	AG09319	gingival:	n/a
40	chr2:97426602-97426652	HRPEpiC	eye:	n/a
41	chr2:97426598-97426648	AG04450	lung:	fetal
42	chr2:97426602-97426652	ovcar-3	ovarian:	n/a
43	chr2:97426598-97426648	NT2-D1	testis:	n/a
44	chr2:97426598-97426648	HNPCEpiC	eye:	n/a
45	chr2:97426602-97426652	MCF10A-Er-Src	breast:	n/a
46	chr2:97426598-97426648	K562	blood:	n/a
47	chr2:97426598-97426648	NB4	blood:	n/a
48	chr2:97426598-97426648	MCF10A-Er-Src	breast:	n/a
49	chr2:97426598-97426648	AoSMC	blood vessel:	n/a
50	chr2:97426598-97426648	SAEC	small airway:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97300473..97305040-chr2:97425563..97430425,4	MCF-7	breast:
2	chr14:34930899..34931823-chr2:97425912..97426737,2	Hela-S3	cervix:
3	chr2:96990031..96992678-chr2:97425792..97428161,2	K562	blood:
4	chr2:97399050..97401934-chr2:97425434..97428071,2	MCF-7	breast:
5	chr2:97268720..97275117-chr2:97424272..97429412,8	MCF-7	breast:
6	chr2:97358845..97361710-chr2:97424992..97426847,2	K562	blood:
7	chr2:97404813..97407675-chr2:97425727..97428415,3	K562	blood:
8	chr14:20923224..20923843-chr2:97426397..97427093,2	Hela-S3	cervix:
9	chr15:65596846..65597612-chr2:97426220..97426721,2	Hela-S3	cervix:
10	chr2:97425678..97429518-chr2:97479689..97484495,7	MCF-7	breast:
11	chr2:97425294..97427081-chr2:97533526..97535772,2	K562	blood:
12	chr2:97299733..97305587-chr2:97425305..97429139,7	K562	blood:
13	chr2:97426251..97427245-chr3:20227662..20228331,2	Hela-S3	cervix:
14	chr2:97299733..97305587-chr2:97422203..97428186,8	K562	blood:
15	chr2:97426212..97427746-chr2:97532479..97534253,2	MCF-7	breast:
16	chr2:97426031..97428759-chr2:97617125..97619977,2	MCF-7	breast:
17	chr2:97403401..97407119-chr2:97425023..97428100,7	MCF-7	breast:
18	chr2:97402906..97407899-chr2:97425229..97430147,10	MCF-7	breast:
19	chr11:808341..811136-chr2:97426419..97428883,2	K562	blood:
20	chr19:59057645..59060088-chr2:97425289..97427469,2	MCF-7	breast:
21	chr2:97426560..97429669-chr2:97487357..97491316,3	MCF-7	breast:
22	chr2:97405153..97407675-chr2:97425109..97427390,3	K562	blood:
23	chr2:97301517..97305285-chr2:97426115..97429843,6	MCF-7	breast:

Variant related genes	Relation type
CNNM4	TF binding region
CNNM4	CpG island
ENSG00000129810	Chromatin interaction
ENSG00000177600	Chromatin interaction
ENSG00000165389	Chromatin interaction
ENSG00000114982	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000092094	Chromatin interaction
ENSG00000249715	Chromatin interaction
ENSG00000177595	Chromatin interaction
ENSG00000100823	Chromatin interaction
ENSG00000130726	Chromatin interaction
ENSG00000198885	Chromatin interaction
ENSG00000114988	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	nsv834307	chr2:97321447-97479266	Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
14	esv3438902	chr2:97425450-97427998	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
15	esv3445643	chr2:97425775-97427773	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97425800-97426800	Enhancers	Fetal Heart	heart
2	chr2:97425800-97426800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr2:97426000-97426800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:97426000-97427000	Active TSS	Brain Anterior Caudate	brain
5	chr2:97426000-97427000	Active TSS	Brain Germinal Matrix	brain
6	chr2:97426000-97427000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:97426000-97427200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr2:97426000-97427200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:97426000-97427200	Active TSS	Brain Angular Gyrus	brain
10	chr2:97426000-97427200	Active TSS	Brain Hippocampus Middle	brain
11	chr2:97426000-97427200	Active TSS	Brain Substantia Nigra	brain
12	chr2:97426000-97427200	Active TSS	Fetal Brain Female	brain
13	chr2:97426000-97427200	Active TSS	Ovary	ovary
14	chr2:97426000-97427200	Active TSS	Psoas Muscle	Psoas
15	chr2:97426000-97427400	Active TSS	Fetal Kidney	kidney
16	chr2:97426000-97427600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:97426200-97426800	Active TSS	Primary T cells from cord blood	blood
18	chr2:97426200-97427000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:97426200-97427000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr2:97426200-97427000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr2:97426200-97427000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:97426200-97427000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:97426200-97427000	Active TSS	Brain Cingulate Gyrus	brain
24	chr2:97426200-97427000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:97426200-97427000	Active TSS	Fetal Lung	lung
26	chr2:97426200-97427000	Active TSS	Lung	lung
27	chr2:97426200-97427000	Active TSS	Spleen	Spleen
28	chr2:97426200-97427000	Active TSS	A549	lung
29	chr2:97426200-97427000	Active TSS	NHLF	lung
30	chr2:97426200-97427200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:97426200-97427200	Active TSS	Gastric	stomach
32	chr2:97426200-97427200	Active TSS	Left Ventricle	heart
33	chr2:97426200-97427200	Active TSS	Rectal Smooth Muscle	rectum
34	chr2:97426200-97427400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:97426200-97427400	Active TSS	Aorta	Aorta
36	chr2:97426200-97427400	Active TSS	Colon Smooth Muscle	Colon
37	chr2:97426200-97427400	Active TSS	Small Intestine	intestine
38	chr2:97426200-97428000	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr2:97426200-97430400	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr2:97426400-97426800	Active TSS	H1 Cell Line	embryonic stem cell
41	chr2:97426400-97426800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:97426400-97426800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:97426400-97426800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:97426400-97426800	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr2:97426400-97426800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:97426400-97426800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:97426400-97426800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:97426400-97426800	Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr2:97426400-97426800	Enhancers	Primary B cells from cord blood	blood
50	chr2:97426400-97426800	Active TSS	Primary T cells fromperipheralblood	blood

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