Variant report

Variant	rs12475433
Chromosome Location	chr2:173293419-173293420
allele	G/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	POLR2A	chr2:173292141-173294851	MCF10A-Er-Src	breast:	n/a	n/a
2	TBP	chr2:173291928-173293848	HepG2	liver:	n/a	n/a
3	MAZ	chr2:173291769-173294408	IMR90	lung:	n/a	chr2:173294307-173294315 chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
4	POLR2A	chr2:173293370-173293669	Hela-S3	cervix:	n/a	n/a
5	SMARCB1	chr2:173291938-173293478	Hela-S3	cervix:	n/a	chr2:173292077-173292086
6	POLR2A	chr2:173293012-173293897	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr2:173292735-173293636	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:173291850-173293649	Hela-S3	cervix:	n/a	n/a
9	HEY1	chr2:173293248-173293912	HepG2	liver:	n/a	n/a
10	TCF12	chr2:173292954-173293670	A549	lung:	n/a	n/a
11	MAX	chr2:173291781-173293601	Hela-S3	cervix:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
12	CREB1	chr2:173291720-173293971	HepG2	liver:	n/a	n/a
13	MBD4	chr2:173292864-173293931	HepG2	liver:	n/a	n/a
14	MAZ	chr2:173291952-173293814	HepG2	liver:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
15	MYC	chr2:173293118-173293492	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr2:173291466-173293613	Raji	blood:	n/a	n/a
17	FOXA2	chr2:173293163-173293846	HepG2	liver:	n/a	n/a
18	NFIC	chr2:173293200-173293954	HepG2	liver:	n/a	n/a
19	MAX	chr2:173291779-173293536	H1-hESC	embryonic stem cell:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
20	E2F6	chr2:173292792-173293553	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr2:173291649-173293591	A549	lung:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972 chr2:173291677-173291688
22	SIN3A	chr2:173291860-173293986	H1-hESC	embryonic stem cell:	n/a	chr2:173292394-173292407
23	E2F4	chr2:173292596-173293673	MCF10A-Er-Src	breast:	n/a	chr2:173292770-173292782 chr2:173292729-173292739 chr2:173293622-173293629 chr2:173292759-173292773 chr2:173292756-173292770
24	SIN3AK20	chr2:173293295-173293709	PANC-1	pancreas:	n/a	n/a
25	CHD2	chr2:173292952-173293703	H1-hESC	embryonic stem cell:	n/a	n/a
26	EP300	chr2:173293228-173293673	HepG2	liver:	n/a	n/a
27	POLR2A	chr2:173291822-173294773	HepG2	liver:	n/a	n/a
28	MAX	chr2:173291621-173293660	HCT-116	colon:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972 chr2:173291677-173291688
29	HEY1	chr2:173293144-173293924	HepG2	liver:	n/a	n/a
30	RAD21	chr2:173292822-173293436	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr2:173291640-173293860	HepG2	liver:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972 chr2:173291677-173291688
32	RCOR1	chr2:173291709-173293800	HepG2	liver:	n/a	n/a
33	YY1	chr2:173293285-173293558	HCT-116	colon:	n/a	n/a
34	TCF7L2	chr2:173291868-173293479	HCT-116	colon:	n/a	n/a
35	MXI1	chr2:173291822-173293667	HepG2	liver:	n/a	n/a
36	CTCF	chr2:173291749-173293808	A549	lung:	n/a	chr2:173292343-173292356 chr2:173292474-173292487
37	SMC3	chr2:173291925-173293650	Hela-S3	cervix:	n/a	n/a
38	SIN3AK20	chr2:173293256-173293745	HepG2	liver:	n/a	n/a
39	TCF12	chr2:173293173-173293578	H1-hESC	embryonic stem cell:	n/a	n/a
40	FOXA1	chr2:173293064-173293821	HepG2	liver:	n/a	n/a
41	CHD1	chr2:173293408-173293833	H1-hESC	embryonic stem cell:	n/a	n/a
42	CHD2	chr2:173293198-173293538	HepG2	liver:	n/a	n/a
43	CHD2	chr2:173291973-173293551	Hela-S3	cervix:	n/a	n/a
44	RFX5	chr2:173292821-173293447	Hela-S3	cervix:	n/a	n/a
45	FOXA1	chr2:173293151-173293712	HepG2	liver:	n/a	n/a
46	MAZ	chr2:173291938-173293757	Hela-S3	cervix:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
47	RAD21	chr2:173292798-173293442	A549	lung:	n/a	n/a
48	MAX	chr2:173291687-173293603	H1-hESC	embryonic stem cell:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
49	TCF7L2	chr2:173292948-173293818	Hela-S3	cervix:	n/a	n/a
50	FOXA1	chr2:173292808-173293722	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:173293392-173293442	Hepatocyte	liver:	n/a
2	chr2:173293392-173293442	Hela-S3	cervix:	n/a
3	chr2:173293392-173293442	GM12892	blood:	n/a
4	chr2:173293392-173293442	Jurkat	blood:	n/a
5	chr2:173293392-173293442	NH-A	brain:	n/a
6	chr2:173293392-173293442	GM12878	blood:	n/a
7	chr2:173293392-173293442	IMR90	lung:	fetal
8	chr2:173293392-173293442	HUVEC	blood vessel:	n/a
9	chr2:173293392-173293442	HRE	kidney:	n/a
10	chr2:173293392-173293442	HMEC	breast:	n/a
11	chr2:173293392-173293442	RPTEC	kidney:	n/a
12	chr2:173293392-173293442	SK-N-MC	brain:	n/a
13	chr2:173293392-173293442	Caco-2	colon:	n/a
14	chr2:173293392-173293442	CMK	blood:	n/a
15	chr2:173293392-173293442	HNPCEpiC	eye:	n/a
16	chr2:173293392-173293442	HEEpiC	esophagus:	n/a
17	chr2:173293392-173293442	K562	blood:	n/a
18	chr2:173293392-173293442	U87	brain:	n/a
19	chr2:173293392-173293442	HIPEpiC	eye:	n/a
20	chr2:173293392-173293442	HCF	heart:	n/a
21	chr2:173293392-173293442	T-47D	breast:	n/a
22	chr2:173293392-173293442	SKMC	muscle:	n/a
23	chr2:173293392-173293442	HCM	heart:	n/a
24	chr2:173293392-173293442	HCPEpiC	choroid plexus:	n/a
25	chr2:173293392-173293442	NT2-D1	testis:	n/a
26	chr2:173293392-173293442	HRCEpiC	kidney:	n/a
27	chr2:173293392-173293442	LNCaP	prostate:	n/a
28	chr2:173293392-173293442	BE2_C	brain:	n/a
29	chr2:173293392-173293442	AG09309	skin:	n/a
30	chr2:173293392-173293442	A549	lung:	n/a
31	chr2:173293392-173293442	HRPEpiC	eye:	n/a
32	chr2:173293392-173293442	AG09319	gingival:	n/a
33	chr2:173293392-173293442	GM12891	blood:	n/a
34	chr2:173293392-173293442	SK-N-SH	brain:	n/a
35	chr2:173293392-173293442	PANC-1	pancreas:	n/a
36	chr2:173293392-173293442	HEK293	kidney:	embryo
37	chr2:173293392-173293442	NHBE	bronchial:	n/a
38	chr2:173293392-173293442	GM06990	blood:	n/a
39	chr2:173293392-173293442	HL-60	blood:	n/a
40	chr2:173293392-173293442	HAEpiC	amniotic membrane:	n/a
41	chr2:173293392-173293442	MCF10A-Er-Src	breast:	n/a
42	chr2:173293392-173293442	BJ	skin:	n/a
43	chr2:173293392-173293442	AG04449	skin:	fetal
44	chr2:173293392-173293442	PFSK-1	brain:	n/a
45	chr2:173293392-173293442	AoSMC	blood vessel:	n/a
46	chr2:173293392-173293442	AG10803	skin:	n/a
47	chr2:173293392-173293442	ECC-1	luminal epithelium:	n/a
48	chr2:173293392-173293442	MCF-7	breast:	n/a
49	chr2:173293392-173293442	AG04450	lung:	fetal
50	chr2:173293392-173293442	H1-hESC	embryonic stem cell:	embryo

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:98897396..98898383-chr2:173292432..173293421,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000226963	TF binding region
ENSG00000226963	CpG island
ENSG00000245017	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1001926	0.83[ASN][1000 genomes]
rs2008518	0.82[ASN][1000 genomes]
rs2178476	0.83[ASN][1000 genomes]
rs2272496	0.83[ASN][1000 genomes]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3322868	chr2:173291131-173293679	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173291600-173293600	Active TSS	A549	lung
2	chr2:173291600-173294000	Active TSS	HSMMtube	muscle
3	chr2:173291600-173294400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr2:173291600-173295200	Active TSS	Rectal Smooth Muscle	rectum
5	chr2:173291800-173293600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
6	chr2:173291800-173293800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:173291800-173293800	Bivalent/Poised TSS	Osteobl	bone
8	chr2:173291800-173294200	Active TSS	HSMM	muscle
9	chr2:173291800-173294400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr2:173291800-173294600	Active TSS	Brain Substantia Nigra	brain
11	chr2:173291800-173294600	Active TSS	Gastric	stomach
12	chr2:173291800-173295200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:173292000-173293600	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr2:173292000-173293600	Active TSS	Fetal Heart	heart
15	chr2:173292000-173293600	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr2:173292000-173293600	Active TSS	Hela-S3	cervix
17	chr2:173292000-173293600	Active TSS	NHLF	lung
18	chr2:173292000-173293800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr2:173292000-173293800	Active TSS	Fetal Kidney	kidney
20	chr2:173292000-173294000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr2:173292000-173294000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr2:173292000-173294000	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr2:173292000-173294000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:173292000-173294000	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr2:173292000-173294200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr2:173292000-173294200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr2:173292000-173294200	Active TSS	Aorta	Aorta
28	chr2:173292000-173294200	Active TSS	Psoas Muscle	Psoas
29	chr2:173292000-173294400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:173292000-173294400	Active TSS	Primary T cells from cord blood	blood
31	chr2:173292000-173294400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr2:173292000-173294400	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr2:173292000-173294400	Active TSS	Brain Angular Gyrus	brain
34	chr2:173292000-173294400	Active TSS	Ovary	ovary
35	chr2:173292000-173294600	Active TSS	Pancreas	Pancrea
36	chr2:173292000-173294600	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr2:173292000-173294800	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr2:173292000-173294800	Active TSS	Brain Hippocampus Middle	brain
39	chr2:173292000-173295200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr2:173292000-173295600	Active TSS	Fetal Intestine Large	intestine
41	chr2:173292000-173296600	Active TSS	Right Atrium	heart
42	chr2:173292200-173293600	Active TSS	Muscle Satellite Cultured Cells	--
43	chr2:173292200-173293600	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr2:173292200-173293800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:173292200-173293800	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr2:173292200-173293800	Active TSS	NHDF-Ad	bronchial
47	chr2:173292200-173294000	Active TSS	H1 Cell Line	embryonic stem cell
48	chr2:173292200-173294000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:173292200-173294000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr2:173292200-173294200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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