Variant report

Variant	rs555954686
Chromosome Location	chr2:173292472-173292473
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	POLR2A	chr2:173292141-173294851	MCF10A-Er-Src	breast:	n/a	n/a
2	YY1	chr2:173292226-173292765	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:173292006-173293150	HUVEC	blood vessel:	n/a	n/a
4	MAX	chr2:173291801-173293195	NB4	blood:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
5	SIN3AK20	chr2:173291950-173293096	PANC-1	pancreas:	n/a	n/a
6	FOXA1	chr2:173291979-173292750	HepG2	liver:	n/a	n/a
7	ZNF263	chr2:173291911-173292680	HEK293-T-REx	kidney:	n/a	n/a
8	TBP	chr2:173291928-173293848	HepG2	liver:	n/a	n/a
9	TCF12	chr2:173291846-173293252	ECC-1	luminal epithelium:	n/a	n/a
10	MAZ	chr2:173291769-173294408	IMR90	lung:	n/a	chr2:173294307-173294315 chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
11	MYC	chr2:173292333-173292501	HUVEC	blood vessel:	n/a	n/a
12	REST	chr2:173292201-173292502	SK-N-SH	brain:	n/a	n/a
13	HMGN3	chr2:173292059-173292645	K562	blood:	n/a	n/a
14	CTCF	chr2:173292196-173292477	K562	blood:	n/a	chr2:173292343-173292356
15	SMARCB1	chr2:173291938-173293478	Hela-S3	cervix:	n/a	chr2:173292077-173292086
16	POLR2A	chr2:173292248-173292633	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:173291948-173292616	HL-60	blood:	n/a	n/a
18	POLR2A	chr2:173291850-173293649	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr2:173292234-173292507	SK-N-SH	brain:	n/a	n/a
20	TAF1	chr2:173292148-173292541	Hela-S3	cervix:	n/a	n/a
21	EP300	chr2:173291755-173292635	ECC-1	luminal epithelium:	n/a	chr2:173292326-173292342 chr2:173292100-173292116 chr2:173292342-173292358
22	MAX	chr2:173291785-173292624	K562	blood:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
23	YY1	chr2:173291998-173292684	SK-N-SH_RA	brain:	n/a	chr2:173292098-173292112
24	MAX	chr2:173291781-173293601	Hela-S3	cervix:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
25	CREB1	chr2:173291720-173293971	HepG2	liver:	n/a	n/a
26	MAZ	chr2:173291952-173293814	HepG2	liver:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
27	E2F6	chr2:173291703-173292475	H1-hESC	embryonic stem cell:	n/a	chr2:173292261-173292271 chr2:173292349-173292358
28	CTCF	chr2:173292340-173292490	WERI-Rb-1	eye:	n/a	chr2:173292343-173292356 chr2:173292474-173292487
29	POLR2A	chr2:173291913-173292495	HL-60	blood:	n/a	n/a
30	POLR2A	chr2:173292180-173292555	IMR90	lung:	n/a	n/a
31	POLR2A	chr2:173291997-173292910	A549	lung:	n/a	n/a
32	POLR2A	chr2:173291466-173293613	Raji	blood:	n/a	n/a
33	EP300	chr2:173291906-173292591	HepG2	liver:	n/a	chr2:173292326-173292342 chr2:173292100-173292116 chr2:173292342-173292358
34	POLR2A	chr2:173291986-173292552	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:173292050-173292508	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr2:173291815-173292682	H1-neurons	neurons:	n/a	n/a
37	E2F6	chr2:173291606-173292807	H1-hESC	embryonic stem cell:	n/a	chr2:173292770-173292782 chr2:173292261-173292271 chr2:173292729-173292739 chr2:173292759-173292773 chr2:173292756-173292770 chr2:173292349-173292358
38	POLR2A	chr2:173292051-173292857	HUVEC	blood vessel:	n/a	n/a
39	REST	chr2:173292164-173292819	HL-60	blood:	n/a	chr2:173292169-173292179
40	SIN3AK20	chr2:173292009-173292598	HepG2	liver:	n/a	n/a
41	MAX	chr2:173291779-173293536	H1-hESC	embryonic stem cell:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
42	POLR2A	chr2:173292055-173292615	ProgFib	skin:	n/a	n/a
43	MAX	chr2:173291649-173293591	A549	lung:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972 chr2:173291677-173291688
44	SIN3A	chr2:173291860-173293986	H1-hESC	embryonic stem cell:	n/a	chr2:173292394-173292407
45	POLR2A	chr2:173292158-173292627	MCF-7	breast:	n/a	n/a
46	MYC	chr2:173291768-173293391	MCF10A-Er-Src	breast:	n/a	chr2:173291961-173291971 chr2:173291962-173291969 chr2:173291963-173291972
47	MAZ	chr2:173292084-173292548	K562	blood:	n/a	n/a
48	RAD21	chr2:173291972-173292552	HepG2	liver:	n/a	chr2:173292418-173292430
49	CHD2	chr2:173292231-173292515	HepG2	liver:	n/a	n/a
50	POLR2A	chr2:173292070-173292616	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173292234..173292806-chr4:75230715..75231293,2	HCT-116	colon:
2	chr12:98897396..98898383-chr2:173292432..173293421,2	Hela-S3	cervix:

Variant related genes	Relation type
ITGA6	TF binding region
ENSG00000124882	Chromatin interaction
ENSG00000245017	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	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173291600-173293200	Flanking Bivalent TSS/Enh	Dnd41	blood
2	chr2:173291600-173293600	Active TSS	A549	lung
3	chr2:173291600-173294000	Active TSS	HSMMtube	muscle
4	chr2:173291600-173294400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr2:173291600-173295200	Active TSS	Rectal Smooth Muscle	rectum
6	chr2:173291800-173292600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:173291800-173292800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr2:173291800-173293000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
9	chr2:173291800-173293000	Active TSS	Placenta Amnion	Placenta Amnion
10	chr2:173291800-173293600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
11	chr2:173291800-173293800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:173291800-173293800	Bivalent/Poised TSS	Osteobl	bone
13	chr2:173291800-173294200	Active TSS	HSMM	muscle
14	chr2:173291800-173294400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr2:173291800-173294600	Active TSS	Brain Substantia Nigra	brain
16	chr2:173291800-173294600	Active TSS	Gastric	stomach
17	chr2:173291800-173295200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:173292000-173292600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:173292000-173292800	Bivalent/Poised TSS	K562	blood
20	chr2:173292000-173293000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:173292000-173293000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:173292000-173293000	Active TSS	Primary T cells fromperipheralblood	blood
23	chr2:173292000-173293000	Bivalent/Poised TSS	Fetal Stomach	stomach
24	chr2:173292000-173293000	Active TSS	Spleen	Spleen
25	chr2:173292000-173293000	Active TSS	HUVEC	blood vessel
26	chr2:173292000-173293200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:173292000-173293200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
28	chr2:173292000-173293200	Active TSS	Fetal Brain Female	brain
29	chr2:173292000-173293200	Active TSS	Fetal Intestine Small	intestine
30	chr2:173292000-173293200	Active TSS	Thymus	Thymus
31	chr2:173292000-173293400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr2:173292000-173293400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:173292000-173293400	Active TSS	Fetal Lung	lung
34	chr2:173292000-173293600	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr2:173292000-173293600	Active TSS	Fetal Heart	heart
36	chr2:173292000-173293600	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr2:173292000-173293600	Active TSS	Hela-S3	cervix
38	chr2:173292000-173293600	Active TSS	NHLF	lung
39	chr2:173292000-173293800	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr2:173292000-173293800	Active TSS	Fetal Kidney	kidney
41	chr2:173292000-173294000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr2:173292000-173294000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr2:173292000-173294000	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr2:173292000-173294000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:173292000-173294000	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr2:173292000-173294200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr2:173292000-173294200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr2:173292000-173294200	Active TSS	Aorta	Aorta
49	chr2:173292000-173294200	Active TSS	Psoas Muscle	Psoas
50	chr2:173292000-173294400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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