Variant report

Variant	rs2459221
Chromosome Location	chr4:56275947-56275948
allele	A/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	RAD21	chr4:56275642-56276012	SK-N-SH_RA	brain:	n/a	n/a
2	YY1	chr4:56275622-56276017	GM12878	blood:	n/a	n/a
3	CTCF	chr4:56275576-56276049	GM12878	blood:	n/a	n/a
4	RAD21	chr4:56275584-56275982	HepG2	liver:	n/a	n/a
5	CTCF	chr4:56275860-56276010	HCT-116	colon:	n/a	n/a
6	MAFK	chr4:56275832-56276358	IMR90	lung:	n/a	chr4:56276163-56276174 chr4:56276161-56276175 chr4:56276158-56276173 chr4:56276153-56276173 chr4:56276158-56276174 chr4:56276163-56276174
7	RAD21	chr4:56275609-56276020	GM12878	blood:	n/a	n/a
8	RUNX3	chr4:56275612-56275991	GM12878	blood:	n/a	n/a
9	RAD21	chr4:56275524-56275994	HCT-116	colon:	n/a	n/a
10	EBF1	chr4:56275541-56276203	GM12878	blood:	n/a	chr4:56275840-56275851
11	POLR2A	chr4:56275912-56275975	HepG2	liver:	n/a	n/a
12	RAD21	chr4:56275626-56275997	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAFK	chr4:56275920-56276329	K562	blood:	n/a	chr4:56276163-56276174 chr4:56276161-56276175 chr4:56276158-56276173 chr4:56276153-56276173 chr4:56276158-56276174 chr4:56276163-56276174
14	RAD21	chr4:56275694-56276026	MCF-7	breast:	n/a	n/a
15	YY1	chr4:56275683-56275997	GM12878	blood:	n/a	n/a
16	TBP	chr4:56275721-56276169	GM12878	blood:	n/a	n/a
17	RFX5	chr4:56275741-56275958	GM12878	blood:	n/a	n/a
18	SMC3	chr4:56275637-56275984	GM12878	blood:	n/a	n/a
19	MAZ	chr4:56275651-56276142	GM12878	blood:	n/a	n/a
20	EBF1	chr4:56275635-56276040	GM12878	blood:	n/a	chr4:56275840-56275851
21	YY1	chr4:56275644-56275972	GM12892	blood:	n/a	n/a
22	RAD21	chr4:56275509-56276027	H1-hESC	embryonic stem cell:	n/a	n/a
23	RUNX3	chr4:56275622-56275996	GM12878	blood:	n/a	n/a
24	EBF1	chr4:56275598-56276262	GM12878	blood:	n/a	chr4:56275840-56275851
25	CHD2	chr4:56275751-56276042	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:56275850-56276023	ProgFib	skin:	n/a	n/a
27	POLR2A	chr4:56275831-56276149	Hela-S3	cervix:	n/a	n/a
28	YY1	chr4:56275601-56275980	GM12892	blood:	n/a	n/a
29	POLR2A	chr4:56275574-56276470	K562	blood:	n/a	n/a
30	ZC3H11A	chr4:56275731-56275976	K562	blood:	n/a	n/a
31	CTCF	chr4:56275467-56276020	A549	lung:	n/a	n/a
32	CUX1	chr4:56275704-56275988	GM12878	blood:	n/a	n/a
33	RAD21	chr4:56275541-56276003	HCT-116	colon:	n/a	n/a
34	MXI1	chr4:56275683-56275985	GM12878	blood:	n/a	n/a
35	RAD21	chr4:56275598-56275994	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZNF143	chr4:56275617-56275987	GM12878	blood:	n/a	n/a
37	YY1	chr4:56275662-56275959	GM12891	blood:	n/a	n/a
38	RAD21	chr4:56275608-56275983	IMR90	lung:	n/a	n/a
39	WRNIP1	chr4:56275600-56276310	GM12878	blood:	n/a	n/a
40	CTCF	chr4:56275632-56275960	K562	blood:	n/a	n/a
41	CTCF	chr4:56275620-56275948	IMR90	lung:	n/a	n/a
42	POLR2A	chr4:56275945-56275992	MCF-7	breast:	n/a	n/a
43	RAD21	chr4:56275637-56275949	GM12878	blood:	n/a	n/a
44	RAD21	chr4:56275593-56275994	GM12878	blood:	n/a	n/a
45	CTCF	chr4:56275628-56275973	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56266974..56269917-chr4:56274406..56277195,2	MCF-7	breast:
2	chr4:56275809..56278262-chr4:56283958..56286779,2	K562	blood:
3	chr4:56274229..56276308-chr4:56282213..56284888,2	MCF-7	breast:
4	chr4:56212034..56214727-chr4:56273890..56277792,4	MCF-7	breast:
5	chr4:56275357..56276969-chr4:56278141..56280146,2	K562	blood:
6	chr4:56275450..56278290-chr4:56412391..56414503,2	K562	blood:
7	chr4:56269741..56272367-chr4:56273938..56276057,3	MCF-7	breast:
8	chr4:56211324..56213872-chr4:56274081..56277036,2	K562	blood:

Variant related genes	Relation type
ENSG00000239040	TF binding region
ENSG00000239040	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000272969	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10011355	1.00[AMR][1000 genomes]
rs10028745	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1158370	1.00[AMR][1000 genomes]
rs13144358	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1844218	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1968771	1.00[AMR][1000 genomes]
rs2130034	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2130037	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2168946	1.00[AMR][1000 genomes]
rs2175641	1.00[AMR][1000 genomes]
rs2412651	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4865009	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs556776	1.00[AMR][1000 genomes]
rs6554250	1.00[AMR][1000 genomes]
rs6855258	1.00[AMR][1000 genomes]
rs6857669	1.00[AMR][1000 genomes]
rs977061	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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 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	chr4:56264800-56282200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:56265600-56281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:56265600-56283800	Weak transcription	Fetal Brain Male	brain
5	chr4:56265600-56286000	Weak transcription	Colonic Mucosa	Colon
6	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:56265800-56281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:56266000-56283200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:56267400-56280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:56267400-56282800	Weak transcription	Small Intestine	intestine
12	chr4:56267400-56283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr4:56267600-56280800	Weak transcription	A549	lung
14	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:56269000-56311400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:56270000-56281000	Weak transcription	Fetal Kidney	kidney
17	chr4:56270200-56281000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:56270200-56281600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:56270200-56282800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:56270400-56277400	Weak transcription	Hela-S3	cervix
21	chr4:56270400-56286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:56271800-56277800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:56272400-56276000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:56272400-56278000	Weak transcription	Esophagus	oesophagus
25	chr4:56272400-56281000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:56272600-56277800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:56272600-56282800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:56273200-56279600	Weak transcription	Fetal Brain Female	brain
29	chr4:56273400-56277600	Weak transcription	HMEC	breast
30	chr4:56273400-56277800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:56273400-56283200	Weak transcription	Brain Germinal Matrix	brain
32	chr4:56273600-56276200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:56273600-56277600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:56273600-56277800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:56273600-56277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:56273600-56277800	Weak transcription	Fetal Intestine Small	intestine
37	chr4:56273600-56277800	Weak transcription	Fetal Stomach	stomach
38	chr4:56273600-56277800	Weak transcription	Lung	lung
39	chr4:56273600-56282200	Weak transcription	Pancreas	Pancrea
40	chr4:56273800-56276800	Weak transcription	Placenta	Placenta
41	chr4:56273800-56281600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:56273800-56283200	Weak transcription	Psoas Muscle	Psoas
43	chr4:56274000-56276000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:56274200-56276000	Enhancers	Brain Substantia Nigra	brain
45	chr4:56274200-56276000	Weak transcription	Fetal Lung	lung
46	chr4:56274200-56276000	Weak transcription	Dnd41	blood
47	chr4:56274200-56276200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:56274200-56276200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:56274200-56276400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr4:56274200-56277400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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