Variant report

Variant	rs56357262
Chromosome Location	chr2:179278077-179278078
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	YY1	chr2:179278059-179278737	GM12892	blood:	n/a	chr2:179278417-179278431 chr2:179278417-179278426 chr2:179278388-179278397 chr2:179278420-179278434 chr2:179278391-179278403
2	POLR2A	chr2:179277940-179279967	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr2:179277875-179278934	H1-hESC	embryonic stem cell:	n/a	n/a
4	RELA	chr2:179277954-179278937	GM15510	blood:	n/a	n/a
5	MAX	chr2:179278009-179279928	A549	lung:	n/a	chr2:179278427-179278437 chr2:179279709-179279718 chr2:179279562-179279573
6	POLR2A	chr2:179278069-179278911	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:179277983-179279758	GM19193	blood:	n/a	n/a
8	SP1	chr2:179278073-179278882	A549	lung:	n/a	chr2:179278640-179278654 chr2:179278363-179278373
9	POLR2A	chr2:179278013-179279854	GM12878	blood:	n/a	n/a
10	HA-E2F1	chr2:179277962-179278797	MCF-7	breast:	n/a	chr2:179278421-179278431 chr2:179278649-179278658 chr2:179278651-179278660 chr2:179278388-179278397
11	POLR2A	chr2:179278028-179278950	U87	brain:	n/a	n/a
12	TAF1	chr2:179278061-179278816	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:179277640-179280115	GM12891	blood:	n/a	n/a
14	POLR2A	chr2:179277690-179279851	GM12878	blood:	n/a	n/a
15	NR2F2	chr2:179277955-179280023	K562	blood:	n/a	n/a
16	POLR2A	chr2:179277974-179279814	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr2:179277985-179279099	GM12892	blood:	n/a	n/a
18	POLR2A	chr2:179277931-179279910	GM12892	blood:	n/a	n/a
19	POLR2A	chr2:179278070-179279831	GM18526	blood:	n/a	n/a
20	RUNX3	chr2:179278009-179278994	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:179277933-179279887	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr2:179277651-179280091	GM12878	blood:	n/a	n/a
23	MAX	chr2:179278020-179278858	K562	blood:	n/a	chr2:179278427-179278437
24	POLR2A	chr2:179278039-179279017	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr2:179277787-179279813	GM12892	blood:	n/a	n/a
26	POLR2A	chr2:179277780-179279867	GM19099	blood:	n/a	n/a
27	POLR2A	chr2:179278059-179278941	GM12891	blood:	n/a	n/a
28	ELF1	chr2:179277967-179278736	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:179278070-179278909	HUVEC	blood vessel:	n/a	n/a
30	YY1	chr2:179278069-179278781	K562	blood:	n/a	chr2:179278417-179278431 chr2:179278417-179278426 chr2:179278388-179278397 chr2:179278420-179278434 chr2:179278391-179278403
31	POLR2A	chr2:179277913-179279863	U87	brain:	n/a	n/a
32	POLR2A	chr2:179277935-179279791	U87	brain:	n/a	n/a
33	POLR2A	chr2:179278051-179279771	Hela-S3	cervix:	n/a	n/a
34	MAX	chr2:179278023-179279027	A549	lung:	n/a	chr2:179278427-179278437
35	MXI1	chr2:179277602-179280107	SK-N-SH	brain:	n/a	n/a
36	RUNX3	chr2:179278075-179278852	GM12878	blood:	n/a	n/a
37	KAP1	chr2:179277734-179280044	HEK293	kidney:	n/a	chr2:179279500-179279508
38	POLR2A	chr2:179277937-179279868	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr2:179278042-179279004	K562	blood:	n/a	n/a
40	TRIM28	chr2:179277959-179279140	K562	blood:	n/a	n/a
41	CREB1	chr2:179278077-179279074	GM12878	blood:	n/a	chr2:179278648-179278661
42	MTA3	chr2:179277919-179279998	GM12878	blood:	n/a	n/a
43	RAD21	chr2:179278056-179280193	SK-N-SH	brain:	n/a	chr2:179279571-179279590 chr2:179278622-179278631
44	PML	chr2:179277978-179280005	GM12878	blood:	n/a	chr2:179279500-179279508
45	POLR2A	chr2:179278053-179278870	Hela-S3	cervix:	n/a	n/a
46	TAF1	chr2:179278018-179278863	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr2:179278046-179278907	GM12891	blood:	n/a	n/a
48	POLR2A	chr2:179278050-179279826	GM18951	blood:	n/a	n/a
49	CBX3	chr2:179278000-179279097	K562	blood:	n/a	n/a
50	POLR2A	chr2:179278072-179278897	H1-hESC	embryonic stem cell:	n/a	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	chr2:179274878..179278568-chr2:179284211..179288261,3	K562	blood:
9	chr2:178974707..178979925-chr2:179277151..179280371,6	K562	blood:
10	chr2:179264734..179266660-chr2:179277060..179279815,2	MCF-7	breast:

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

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10497515	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10497516	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12612917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613303	0.83[AMR][1000 genomes]
rs12615980	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12616943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619401	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16866323	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2276619	0.89[EUR][1000 genomes]
rs2276620	0.89[EUR][1000 genomes]
rs3731756	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3731758	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3765020	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816073	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4491754	0.89[EUR][1000 genomes]
rs55714261	1.00[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];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56165369	0.83[AMR][1000 genomes]
rs56233214	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734446	0.89[EUR][1000 genomes]
rs6736173	0.89[EUR][1000 genomes]
rs6736304	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73034339	0.83[EUR][1000 genomes]
rs73034346	0.89[EUR][1000 genomes]
rs73034359	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73034362	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73034364	0.89[EUR][1000 genomes]
rs73034377	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584420	0.83[AMR][1000 genomes];0.94[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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179277400-179278200	Weak transcription	Fetal Heart	heart
2	chr2:179277600-179278200	Flanking Active TSS	Dnd41	blood
3	chr2:179277600-179278800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:179277600-179279600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:179277600-179279600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:179277600-179279600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:179277600-179279600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:179277600-179279600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:179277600-179279600	Active TSS	Right Atrium	heart
10	chr2:179277600-179280000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:179277600-179280000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr2:179277600-179280200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:179277600-179280400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:179277800-179278200	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr2:179277800-179278200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr2:179277800-179278200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:179277800-179278200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:179277800-179278200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr2:179277800-179278200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr2:179277800-179278200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:179277800-179278200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:179277800-179278200	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr2:179277800-179278200	Enhancers	Fetal Brain Male	brain
24	chr2:179277800-179278200	Flanking Active TSS	HSMMtube	muscle
25	chr2:179277800-179278200	Flanking Active TSS	HUVEC	blood vessel
26	chr2:179277800-179278200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr2:179277800-179278400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr2:179277800-179278800	Active TSS	Fetal Brain Female	brain
29	chr2:179277800-179279000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:179277800-179279000	Active TSS	NH-A	brain
31	chr2:179277800-179279000	Active TSS	Osteobl	bone
32	chr2:179277800-179279200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr2:179277800-179279200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr2:179277800-179279400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr2:179277800-179279600	Active TSS	H1 Cell Line	embryonic stem cell
36	chr2:179277800-179279600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:179277800-179279600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:179277800-179279600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:179277800-179279600	Active TSS	Brain Hippocampus Middle	brain
40	chr2:179277800-179279600	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr2:179277800-179279600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr2:179277800-179279600	Active TSS	Fetal Intestine Large	intestine
43	chr2:179277800-179279600	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr2:179277800-179279600	Active TSS	A549	lung
45	chr2:179277800-179279600	Active TSS	HMEC	breast
46	chr2:179277800-179279600	Active TSS	HSMM	muscle
47	chr2:179277800-179279600	Active TSS	NHDF-Ad	bronchial
48	chr2:179277800-179279600	Active TSS	NHEK	skin
49	chr2:179277800-179279600	Active TSS	NHLF	lung
50	chr2:179277800-179279800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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