Variant report

Variant	rs56233214
Chromosome Location	chr2:179278339-179278340
allele	C/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	YY1	chr2:179278059-179278737	GM12892	blood:	n/a	chr2:179278417-179278431 chr2:179278417-179278426 chr2:179278388-179278397 chr2:179278420-179278434 chr2:179278391-179278403
2	YY1	chr2:179278201-179278793	A549	lung:	n/a	chr2:179278417-179278431 chr2:179278417-179278426 chr2:179278388-179278397 chr2:179278420-179278434 chr2:179278391-179278403
3	BHLHE40	chr2:179278331-179278902	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:179278241-179278763	A549	lung:	n/a	n/a
5	CEBPB	chr2:179278269-179278630	H1-hESC	embryonic stem cell:	n/a	n/a
6	BHLHE40	chr2:179278190-179279076	K562	blood:	n/a	n/a
7	POLR2A	chr2:179277940-179279967	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr2:179277875-179278934	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr2:179278196-179278736	K562	blood:	n/a	chr2:179278427-179278437
10	CREB1	chr2:179278172-179278931	HepG2	liver:	n/a	chr2:179278648-179278661
11	CREB1	chr2:179278115-179278964	GM12878	blood:	n/a	chr2:179278648-179278661
12	MYC	chr2:179278178-179279932	K562	blood:	n/a	chr2:179278427-179278437 chr2:179279709-179279718 chr2:179279562-179279573
13	JUND	chr2:179278317-179278733	H1-hESC	embryonic stem cell:	n/a	chr2:179278650-179278659
14	RELA	chr2:179277954-179278937	GM15510	blood:	n/a	n/a
15	MAX	chr2:179278009-179279928	A549	lung:	n/a	chr2:179278427-179278437 chr2:179279709-179279718 chr2:179279562-179279573
16	POLR2A	chr2:179278251-179278749	A549	lung:	n/a	n/a
17	ATF2	chr2:179278216-179278807	H1-hESC	embryonic stem cell:	n/a	chr2:179278649-179278660
18	TCF7L2	chr2:179278220-179278771	HCT-116	colon:	n/a	n/a
19	MAX	chr2:179278241-179278878	NB4	blood:	n/a	chr2:179278427-179278437
20	ZMIZ1	chr2:179278132-179279958	K562	blood:	n/a	n/a
21	E2F4	chr2:179278288-179278864	MCF10A-Er-Src	breast:	n/a	chr2:179278421-179278431 chr2:179278649-179278658 chr2:179278651-179278660 chr2:179278388-179278397
22	RCOR1	chr2:179278084-179280095	IMR90	lung:	n/a	n/a
23	POLR2A	chr2:179278164-179278834	A549	lung:	n/a	n/a
24	TAF1	chr2:179278096-179278958	A549	lung:	n/a	n/a
25	GATA3	chr2:179278312-179279022	A549	lung:	n/a	n/a
26	MYC	chr2:179278141-179278866	K562	blood:	n/a	chr2:179278427-179278437
27	POLR2A	chr2:179278069-179278911	GM12878	blood:	n/a	n/a
28	MAX	chr2:179278236-179278860	GM12878	blood:	n/a	chr2:179278427-179278437
29	SP1	chr2:179278258-179278740	GM12878	blood:	n/a	chr2:179278640-179278654 chr2:179278363-179278373
30	MAZ	chr2:179278106-179279101	GM12878	blood:	n/a	chr2:179278427-179278437
31	BCLAF1	chr2:179278129-179278918	GM12878	blood:	n/a	chr2:179278413-179278426 chr2:179278385-179278394 chr2:179278422-179278435
32	MXI1	chr2:179278301-179278880	Hela-S3	cervix:	n/a	n/a
33	CREB1	chr2:179278206-179280044	K562	blood:	n/a	chr2:179278648-179278661
34	POLR2A	chr2:179278137-179278797	PFSK-1	brain:	n/a	n/a
35	ELF1	chr2:179278096-179278630	GM12878	blood:	n/a	n/a
36	YY1	chr2:179278124-179278724	H1-hESC	embryonic stem cell:	n/a	chr2:179278417-179278431 chr2:179278417-179278426 chr2:179278388-179278397 chr2:179278420-179278434 chr2:179278391-179278403
37	POLR2A	chr2:179278138-179278932	NB4	blood:	n/a	n/a
38	ELF1	chr2:179278115-179278547	K562	blood:	n/a	n/a
39	POLR2A	chr2:179277983-179279758	GM19193	blood:	n/a	n/a
40	POLR2A	chr2:179278139-179279935	K562	blood:	n/a	n/a
41	RCOR1	chr2:179278254-179278966	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:179278100-179278904	K562	blood:	n/a	n/a
43	ATF2	chr2:179278111-179278953	GM12878	blood:	n/a	chr2:179278649-179278660
44	TBL1XR1	chr2:179278268-179278996	GM12878	blood:	n/a	n/a
45	SIN3AK20	chr2:179278123-179278801	SK-N-SH	brain:	n/a	n/a
46	CTCF	chr2:179278180-179278470	HCPEpiC	choroid plexus:	n/a	chr2:179278283-179278292
47	POLR2A	chr2:179278103-179278891	K562	blood:	n/a	n/a
48	CTCF	chr2:179278200-179278350	RPTEC	kidney:	n/a	chr2:179278283-179278292
49	CCNT2	chr2:179278239-179278788	K562	blood:	n/a	n/a
50	E2F6	chr2:179278081-179278935	A549	lung:	n/a	chr2:179278421-179278431 chr2:179278649-179278658 chr2:179278651-179278660 chr2:179278388-179278397

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:179278332-179278382	HCT-116	colon:	n/a
2	chr2:179278332-179278382	AG10803	skin:	n/a
3	chr2:179278332-179278382	HMEC	breast:	n/a
4	chr2:179278332-179278382	HCM	heart:	n/a
5	chr2:179278332-179278382	RPTEC	kidney:	n/a
6	chr2:179278332-179278382	Jurkat	blood:	n/a
7	chr2:179278332-179278382	SKMC	muscle:	n/a
8	chr2:179278332-179278382	PANC-1	pancreas:	n/a
9	chr2:179278332-179278382	SK-N-MC	brain:	n/a
10	chr2:179278332-179278382	PFSK-1	brain:	n/a
11	chr2:179278332-179278382	NB4	blood:	n/a
12	chr2:179278332-179278382	GM06990	blood:	n/a
13	chr2:179278332-179278382	SK-N-SH	brain:	n/a
14	chr2:179278332-179278382	HEK293	kidney:	embryo
15	chr2:179278332-179278382	Caco-2	colon:	n/a
16	chr2:179278332-179278382	NHDF-neo	bronchial:	n/a
17	chr2:179278332-179278382	U87	brain:	n/a
18	chr2:179278332-179278382	AoSMC	blood vessel:	n/a
19	chr2:179278332-179278382	HL-60	blood:	n/a
20	chr2:179278332-179278382	HNPCEpiC	eye:	n/a
21	chr2:179278332-179278382	SK-N-SH_RA	brain:	n/a
22	chr2:179278332-179278382	GM12891	blood:	n/a
23	chr2:179278332-179278382	MCF-7	breast:	n/a
24	chr2:179278332-179278382	BE2_C	brain:	n/a
25	chr2:179278332-179278382	HRPEpiC	eye:	n/a
26	chr2:179278332-179278382	HRE	kidney:	n/a
27	chr2:179278332-179278382	A549	lung:	n/a
28	chr2:179278332-179278382	HCF	heart:	n/a
29	chr2:179278332-179278382	AG09309	skin:	n/a
30	chr2:179278332-179278382	AG04449	skin:	fetal
31	chr2:179278332-179278382	HUVEC	blood vessel:	n/a
32	chr2:179278332-179278382	IMR90	lung:	fetal
33	chr2:179278332-179278382	HIPEpiC	eye:	n/a
34	chr2:179278332-179278382	ovcar-3	ovarian:	n/a
35	chr2:179278332-179278382	ECC-1	luminal epithelium:	n/a
36	chr2:179278332-179278382	Hepatocyte	liver:	n/a
37	chr2:179278332-179278382	T-47D	breast:	n/a
38	chr2:179278332-179278382	HPAEpiC	pulmonary alveolar:	n/a
39	chr2:179278332-179278382	AG09319	gingival:	n/a
40	chr2:179278332-179278382	LNCaP	prostate:	n/a
41	chr2:179278332-179278382	NT2-D1	testis:	n/a
42	chr2:179278332-179278382	BJ	skin:	n/a
43	chr2:179278332-179278382	GM19239	blood:	n/a
44	chr2:179278332-179278382	NH-A	brain:	n/a
45	chr2:179278332-179278382	HRCEpiC	kidney:	n/a
46	chr2:179278332-179278382	HEEpiC	esophagus:	n/a
47	chr2:179278332-179278382	CMK	blood:	n/a
48	chr2:179278332-179278382	Hela-S3	cervix:	n/a
49	chr2:179278332-179278382	HepG2	liver:	n/a
50	chr2:179278332-179278382	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:178974133..178981122-chr2:179276785..179281060,9	K562	blood:
2	chr2:179276440..179278357-chr2:179314496..179316084,2	MCF-7	breast:
3	chr2:179156403..179158773-chr2:179276903..179278454,2	K562	blood:
4	chr2:179277034..179278552-chr2:179314324..179316959,2	K562	blood:
5	chr2:179276988..179281129-chr2:179311895..179317764,7	MCF-7	breast:
6	chr2:179277180..179281325-chr2:179314213..179317479,5	K562	blood:
7	chr2:179277322..179281063-chr2:179341771..179345640,5	K562	blood:
8	chr2:179278151..179280958-chr2:179342121..179344961,4	K562	blood:
9	chr2:179274878..179278568-chr2:179284211..179288261,3	K562	blood:
10	chr2:178974707..178979925-chr2:179277151..179280371,6	K562	blood:
11	chr2:179264734..179266660-chr2:179277060..179279815,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223960	TF binding region
ENSG00000223960	CpG island
ENSG00000079150	Chromatin interaction
ENSG00000155636	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000260931	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10497515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10497516	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12612917	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613131	0.83[AMR][1000 genomes]
rs12613303	1.00[AMR][1000 genomes]
rs12615980	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12616943	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16866323	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276619	0.94[EUR][1000 genomes]
rs2276620	0.94[EUR][1000 genomes]
rs3731756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3731758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3765020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4491754	0.94[EUR][1000 genomes]
rs55714261	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55821514	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs56065555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56165369	1.00[AMR][1000 genomes]
rs56357262	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56367852	0.83[AMR][1000 genomes]
rs6734446	0.94[EUR][1000 genomes]
rs6736173	0.94[EUR][1000 genomes]
rs6736304	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73034339	0.88[EUR][1000 genomes]
rs73034346	0.94[EUR][1000 genomes]
rs73034359	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73034362	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73034364	0.94[EUR][1000 genomes]
rs73034377	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 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	chr2:179277600-179278800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:179277600-179279600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:179277600-179279600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr2:179277600-179279600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:179277600-179279600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:179277600-179279600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:179277600-179279600	Active TSS	Right Atrium	heart
8	chr2:179277600-179280000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:179277600-179280000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr2:179277600-179280200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:179277600-179280400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:179277800-179278400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr2:179277800-179278800	Active TSS	Fetal Brain Female	brain
14	chr2:179277800-179279000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:179277800-179279000	Active TSS	NH-A	brain
16	chr2:179277800-179279000	Active TSS	Osteobl	bone
17	chr2:179277800-179279200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr2:179277800-179279200	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr2:179277800-179279400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr2:179277800-179279600	Active TSS	H1 Cell Line	embryonic stem cell
21	chr2:179277800-179279600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:179277800-179279600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:179277800-179279600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:179277800-179279600	Active TSS	Brain Hippocampus Middle	brain
25	chr2:179277800-179279600	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr2:179277800-179279600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr2:179277800-179279600	Active TSS	Fetal Intestine Large	intestine
28	chr2:179277800-179279600	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr2:179277800-179279600	Active TSS	A549	lung
30	chr2:179277800-179279600	Active TSS	HMEC	breast
31	chr2:179277800-179279600	Active TSS	HSMM	muscle
32	chr2:179277800-179279600	Active TSS	NHDF-Ad	bronchial
33	chr2:179277800-179279600	Active TSS	NHEK	skin
34	chr2:179277800-179279600	Active TSS	NHLF	lung
35	chr2:179277800-179279800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:179277800-179279800	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:179277800-179279800	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:179277800-179279800	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr2:179277800-179279800	Active TSS	Muscle Satellite Cultured Cells	--
40	chr2:179277800-179279800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:179277800-179279800	Active TSS	Brain Angular Gyrus	brain
42	chr2:179277800-179279800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:179277800-179279800	Active TSS	Rectal Smooth Muscle	rectum
44	chr2:179277800-179279800	Active TSS	Thymus	Thymus
45	chr2:179277800-179279800	Active TSS	GM12878-XiMat	blood
46	chr2:179277800-179280000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr2:179277800-179280000	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr2:179277800-179280000	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr2:179277800-179280000	Active TSS	Brain Anterior Caudate	brain
50	chr2:179277800-179280200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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