Variant report

Variant	rs17046804
Chromosome Location	chr2:55509449-55509450
allele	C/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	TCF12	chr2:55508928-55510157	A549	lung:	n/a	n/a
2	CTCF	chr2:55509447-55509570	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:55509088-55510099	GM15510	blood:	n/a	n/a
4	POLR2A	chr2:55509203-55509948	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:55509126-55510107	K562	blood:	n/a	n/a
6	TRIM28	chr2:55508990-55509887	K562	blood:	n/a	n/a
7	MTA3	chr2:55509295-55509665	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:55508951-55509779	A549	lung:	n/a	n/a
9	POLR2A	chr2:55508732-55510140	GM12878	blood:	n/a	n/a
10	MAX	chr2:55509043-55509956	MCF-7	breast:	n/a	n/a
11	GABPA	chr2:55509074-55509755	K562	blood:	n/a	n/a
12	E2F6	chr2:55508693-55510136	A549	lung:	n/a	chr2:55509235-55509245
13	GABPA	chr2:55509003-55509905	A549	lung:	n/a	n/a
14	POLR2A	chr2:55508730-55510913	HepG2	liver:	n/a	n/a
15	E2F6	chr2:55508497-55509857	H1-hESC	embryonic stem cell:	n/a	chr2:55509235-55509245
16	CHD2	chr2:55509195-55510039	GM12878	blood:	n/a	chr2:55509325-55509335
17	ATF3	chr2:55509128-55509706	A549	lung:	n/a	n/a
18	POLR2A	chr2:55508893-55510045	PFSK-1	brain:	n/a	n/a
19	E2F6	chr2:55509047-55509706	A549	lung:	n/a	chr2:55509235-55509245
20	NFATC1	chr2:55508955-55510042	GM12878	blood:	n/a	n/a
21	JUND	chr2:55509184-55509518	H1-hESC	embryonic stem cell:	n/a	chr2:55509241-55509250
22	POLR2A	chr2:55509086-55509822	GM12891	blood:	n/a	n/a
23	TEAD4	chr2:55509250-55509687	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr2:55509189-55509947	H1-hESC	embryonic stem cell:	n/a	n/a
25	YY1	chr2:55509271-55509975	HepG2	liver:	n/a	chr2:55509430-55509441 chr2:55509747-55509763
26	MYC	chr2:55509195-55509783	MCF-7	breast:	n/a	n/a
27	ELF1	chr2:55509171-55509628	A549	lung:	n/a	chr2:55509377-55509386
28	STAT1	chr2:55509224-55509564	GM12878	blood:	n/a	n/a
29	REST	chr2:55509025-55509880	HepG2	liver:	n/a	chr2:55509729-55509742
30	MAX	chr2:55509192-55509796	HepG2	liver:	n/a	n/a
31	CHD2	chr2:55509175-55509648	HepG2	liver:	n/a	chr2:55509325-55509335
32	TAF1	chr2:55508999-55509917	ECC-1	luminal epithelium:	n/a	n/a
33	EP300	chr2:55509354-55510075	GM12878	blood:	n/a	chr2:55509378-55509394
34	TAF7	chr2:55509005-55509795	H1-hESC	embryonic stem cell:	n/a	n/a
35	ELF1	chr2:55509145-55509767	A549	lung:	n/a	chr2:55509377-55509386
36	RELA	chr2:55509005-55509952	GM15510	blood:	n/a	n/a
37	MAZ	chr2:55509210-55509702	GM12878	blood:	n/a	n/a
38	MAX	chr2:55508988-55509955	ECC-1	luminal epithelium:	n/a	n/a
39	TAF1	chr2:55509222-55509673	GM12891	blood:	n/a	n/a
40	POLR2A	chr2:55508992-55510004	HUVEC	blood vessel:	n/a	n/a
41	SMC3	chr2:55509294-55509654	GM12878	blood:	n/a	n/a
42	MYBL2	chr2:55508831-55510206	HepG2	liver:	n/a	n/a
43	ELF1	chr2:55509198-55509571	K562	blood:	n/a	chr2:55509377-55509386
44	YY1	chr2:55509167-55509784	GM12891	blood:	n/a	chr2:55509430-55509441 chr2:55509747-55509763
45	MYC	chr2:55509281-55509632	MCF-7	breast:	n/a	n/a
46	STAT5A	chr2:55508983-55510024	GM12878	blood:	n/a	n/a
47	MYC	chr2:55509263-55509462	K562	blood:	n/a	n/a
48	MAFK	chr2:55509424-55509773	HepG2	liver:	n/a	n/a
49	YY1	chr2:55509149-55509903	ECC-1	luminal epithelium:	n/a	chr2:55509430-55509441 chr2:55509747-55509763
50	E2F6	chr2:55509221-55509544	K562	blood:	n/a	chr2:55509235-55509245

No.	Distal block	Cell Line	Cell type
1	chr2:55508571..55512777-chr2:55645734..55648780,3	K562	blood:
2	chr2:55508376..55510742-chr2:55843787..55846796,4	K562	blood:
3	chr2:55496311..55498089-chr2:55508225..55509799,2	MCF-7	breast:
4	chr2:55507639..55510296-chr2:55843126..55844712,2	K562	blood:
5	chr2:55494928..55498059-chr2:55506695..55512310,8	K562	blood:
6	chr2:55509373..55510992-chr2:55512785..55514521,3	MCF-7	breast:
7	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:
8	chr2:55507859..55511177-chr2:55645007..55647398,3	K562	blood:
9	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:
10	chr2:55508669..55511212-chr2:55645960..55648569,3	MCF-7	breast:

Variant related genes	Relation type
PRORSD1P	TF binding region
ENSG00000206964	TF binding region
ENSG00000143947	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000206964	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11884873	0.92[YRI][hapmap]
rs11888119	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs11894273	0.84[AFR][1000 genomes]
rs11894557	0.92[YRI][hapmap]
rs11899921	0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs17046882	0.92[YRI][hapmap]
rs17046915	0.93[YRI][hapmap]
rs6710144	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7587178	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 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	chr2:55501000-55517000	Weak transcription	Hela-S3	cervix
2	chr2:55508000-55510600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:55508600-55509600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:55508600-55509800	Active TSS	Primary T cells from cord blood	blood
5	chr2:55508600-55510000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:55508800-55509600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr2:55508800-55509600	Active TSS	Muscle Satellite Cultured Cells	--
8	chr2:55508800-55509600	Active TSS	Brain Germinal Matrix	brain
9	chr2:55508800-55509800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:55508800-55509800	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr2:55508800-55509800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:55508800-55509800	Active TSS	Monocytes-CD14+_RO01746	blood
13	chr2:55508800-55510000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:55508800-55510000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:55508800-55510000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:55508800-55510000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr2:55508800-55510000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:55508800-55510000	Active TSS	Brain Angular Gyrus	brain
19	chr2:55508800-55510000	Active TSS	Brain Cingulate Gyrus	brain
20	chr2:55508800-55510000	Active TSS	Brain Substantia Nigra	brain
21	chr2:55508800-55510000	Active TSS	Thymus	Thymus
22	chr2:55508800-55510000	Active TSS	HSMM	muscle
23	chr2:55508800-55510200	Active TSS	H9 Cell Line	embryonic stem cell
24	chr2:55508800-55510200	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr2:55508800-55510200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr2:55508800-55510200	Active TSS	Brain Anterior Caudate	brain
27	chr2:55508800-55510200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr2:55508800-55510200	Active TSS	Colon Smooth Muscle	Colon
29	chr2:55508800-55510200	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr2:55508800-55510200	Active TSS	Fetal Brain Female	brain
31	chr2:55508800-55510200	Active TSS	Fetal Intestine Small	intestine
32	chr2:55508800-55510200	Active TSS	Psoas Muscle	Psoas
33	chr2:55508800-55510200	Active TSS	HSMMtube	muscle
34	chr2:55508800-55510200	Active TSS	NHDF-Ad	bronchial
35	chr2:55508800-55510200	Active TSS	NHLF	lung
36	chr2:55508800-55510200	Active TSS	Osteobl	bone
37	chr2:55508800-55510400	Active TSS	Brain Hippocampus Middle	brain
38	chr2:55508800-55510400	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr2:55508800-55510400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr2:55508800-55510400	Active TSS	Right Ventricle	heart
41	chr2:55508800-55510400	Active TSS	GM12878-XiMat	blood
42	chr2:55508800-55510600	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr2:55508800-55510600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:55508800-55510600	Active TSS	A549	lung
45	chr2:55508800-55510800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:55508800-55510800	Active TSS	Rectal Smooth Muscle	rectum
47	chr2:55508800-55511000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:55508800-55511000	Active TSS	Right Atrium	heart
49	chr2:55508800-55511400	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr2:55509000-55509600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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