Variant report

Variant	rs56979390
Chromosome Location	chr2:86791002-86791003
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	ELK1	chr2:86789743-86791012	Hela-S3	cervix:	n/a	n/a
2	ATF1	chr2:86790235-86791075	K562	blood:	n/a	n/a
3	MYC	chr2:86789757-86791186	NB4	blood:	n/a	n/a
4	CBX3	chr2:86789902-86791303	K562	blood:	n/a	n/a
5	E2F6	chr2:86789904-86791251	K562	blood:	n/a	chr2:86790613-86790622 chr2:86790670-86790679 chr2:86790668-86790677 chr2:86790626-86790635 chr2:86790932-86790944
6	KAP1	chr2:86789720-86791161	HEK293	kidney:	n/a	n/a
7	RCOR1	chr2:86789745-86791076	Hela-S3	cervix:	n/a	n/a
8	MYBL2	chr2:86789421-86791040	HepG2	liver:	n/a	n/a
9	SMC3	chr2:86789875-86791014	GM12878	blood:	n/a	n/a
10	RELA	chr2:86789720-86791242	GM18951	blood:	n/a	n/a
11	CREB1	chr2:86789697-86791015	GM12878	blood:	n/a	chr2:86790667-86790680
12	MAX	chr2:86789834-86791110	K562	blood:	n/a	n/a
13	POLR2A	chr2:86789199-86791048	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:86789775-86791072	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:86789310-86791036	HUVEC	blood vessel:	n/a	n/a
16	SMARCC1	chr2:86789466-86791076	Hela-S3	cervix:	n/a	n/a
17	HCFC1	chr2:86789596-86791295	Hela-S3	cervix:	n/a	n/a
18	STAT5A	chr2:86789743-86791008	GM12878	blood:	n/a	chr2:86790297-86790317
19	RCOR1	chr2:86789799-86791158	GM12878	blood:	n/a	n/a
20	CREB1	chr2:86789849-86791107	A549	lung:	n/a	chr2:86790667-86790680
21	EP300	chr2:86790172-86791092	GM12878	blood:	n/a	chr2:86790407-86790416
22	MAX	chr2:86789789-86791126	A549	lung:	n/a	n/a
23	USF2	chr2:86790436-86791038	Hela-S3	cervix:	n/a	n/a
24	E2F6	chr2:86790437-86791043	H1-hESC	embryonic stem cell:	n/a	chr2:86790613-86790622 chr2:86790670-86790679 chr2:86790668-86790677 chr2:86790626-86790635 chr2:86790932-86790944
25	NFIC	chr2:86789828-86791030	HepG2	liver:	n/a	n/a
26	MAZ	chr2:86789393-86791145	IMR90	lung:	n/a	n/a
27	MAX	chr2:86789659-86791094	HCT-116	colon:	n/a	n/a
28	MAX	chr2:86789874-86791117	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZKSCAN1	chr2:86789826-86791150	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr2:86789462-86791005	H1-hESC	embryonic stem cell:	n/a	n/a
31	RUNX3	chr2:86789838-86791064	GM12878	blood:	n/a	n/a
32	BCL3	chr2:86789663-86791015	A549	lung:	n/a	chr2:86790055-86790068
33	POLR2A	chr2:86789780-86791196	MCF-7	breast:	n/a	n/a
34	WRNIP1	chr2:86789895-86791350	GM12878	blood:	n/a	n/a
35	NRF1	chr2:86789632-86791010	SK-N-SH	brain:	n/a	chr2:86790625-86790639 chr2:86790007-86790016 chr2:86790609-86790623 chr2:86790627-86790636 chr2:86790614-86790623 chr2:86790612-86790623 chr2:86790625-86790636 chr2:86790625-86790636 chr2:86790611-86790622 chr2:86790612-86790621 chr2:86790612-86790626
36	MAFF	chr2:86790040-86791256	K562	blood:	n/a	n/a
37	CREB1	chr2:86789858-86791040	H1-hESC	embryonic stem cell:	n/a	chr2:86790667-86790680
38	SP1	chr2:86789942-86791030	GM12878	blood:	n/a	chr2:86790074-86790083 chr2:86790072-86790084 chr2:86790072-86790084 chr2:86790073-86790083
39	ZMIZ1	chr2:86789897-86791242	K562	blood:	n/a	n/a
40	TBL1XR1	chr2:86789695-86791031	K562	blood:	n/a	n/a
41	ATF2	chr2:86790253-86791156	H1-hESC	embryonic stem cell:	n/a	n/a
42	ATF2	chr2:86790369-86791028	H1-hESC	embryonic stem cell:	n/a	n/a
43	CEBPB	chr2:86790095-86791061	GM12878	blood:	n/a	n/a
44	KAP1	chr2:86789787-86791250	U2OS	brain:	n/a	n/a
45	MAX	chr2:86789679-86791073	ECC-1	luminal epithelium:	n/a	n/a
46	MAX	chr2:86789899-86791117	H1-hESC	embryonic stem cell:	n/a	n/a
47	EP300	chr2:86789972-86791003	GM12878	blood:	n/a	chr2:86790407-86790416
48	REST	chr2:86789673-86791055	A549	lung:	n/a	n/a
49	E2F6	chr2:86790040-86791307	H1-hESC	embryonic stem cell:	n/a	chr2:86790613-86790622 chr2:86790670-86790679 chr2:86790668-86790677 chr2:86790626-86790635 chr2:86790932-86790944
50	SETDB1	chr2:86790359-86791147	U2OS	brain:	n/a	chr2:86790613-86790622

No.	Distal block	Cell Line	Cell type
1	chr2:86789208..86791396-chr2:86847374..86850220,3	K562	blood:
2	chr2:86788265..86792368-chr2:86847223..86851122,9	MCF-7	breast:
3	chr2:86787885..86791617-chr2:86846945..86852237,10	MCF-7	breast:
4	chr2:86667181..86671352-chr2:86788569..86792016,9	K562	blood:
5	chr2:86675470..86677064-chr2:86789067..86791804,2	K562	blood:
6	chr2:86788830..86791431-chr2:86840608..86843450,2	MCF-7	breast:
7	chr2:86667867..86670714-chr2:86788591..86792016,6	K562	blood:
8	chr2:86768416..86770148-chr2:86788776..86791122,2	K562	blood:
9	chr2:86789208..86791396-chr2:86848677..86850220,2	K562	blood:
10	chr2:86789024..86791664-chr2:87302659..87304185,2	MCF-7	breast:

Variant related genes	Relation type
CHMP3	TF binding region
ENSG00000115548	Chromatin interaction
ENSG00000231259	Chromatin interaction
ENSG00000249884	Chromatin interaction
ENSG00000115561	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11904506	1.00[AMR][1000 genomes]
rs12105337	1.00[AMR][1000 genomes]
rs58337574	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59206006	1.00[AMR][1000 genomes]
rs59274254	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6707701	1.00[AMR][1000 genomes]
rs6758280	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936513	1.00[AMR][1000 genomes]
rs7596624	1.00[AMR][1000 genomes]
rs7596866	1.00[AMR][1000 genomes]
rs7604799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9967845	1.00[AMR][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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86789200-86791200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:86789600-86791200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr2:86789600-86791200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:86789600-86791200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr2:86789600-86791200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr2:86789600-86791200	Active TSS	Fetal Brain Female	brain
7	chr2:86789600-86791200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr2:86789600-86791200	Active TSS	A549	lung
9	chr2:86790600-86791200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:86790600-86791200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:86790600-86791200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:86790600-86791200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr2:86790600-86791200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr2:86790600-86791200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr2:86790600-86791200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr2:86790600-86791200	Flanking Active TSS	Fetal Heart	heart
17	chr2:86790600-86791200	Enhancers	Right Ventricle	heart
18	chr2:86790600-86791200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr2:86790600-86791200	Enhancers	Spleen	Spleen
20	chr2:86790600-86791200	Flanking Active TSS	HepG2	liver
21	chr2:86790600-86791200	Flanking Active TSS	Osteobl	bone
22	chr2:86790600-86791400	Flanking Active TSS	Dnd41	blood
23	chr2:86790600-86791400	Flanking Active TSS	Hela-S3	cervix
24	chr2:86790600-86791800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:86790800-86791200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:86790800-86791200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:86790800-86791200	Enhancers	Primary hematopoietic stem cells	blood
28	chr2:86790800-86791200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:86790800-86791200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr2:86790800-86791200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr2:86790800-86791200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:86790800-86791200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:86790800-86791200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:86790800-86791200	Flanking Active TSS	Liver	Liver
35	chr2:86790800-86791200	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr2:86790800-86791200	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr2:86790800-86791200	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr2:86790800-86791200	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr2:86790800-86791200	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr2:86790800-86791200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr2:86790800-86791200	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr2:86790800-86791200	Enhancers	Pancreas	Pancrea
43	chr2:86790800-86791200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr2:86790800-86791200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr2:86790800-86791200	Flanking Active TSS	GM12878-XiMat	blood
46	chr2:86790800-86791400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:86791000-86791200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
48	chr2:86791000-86791200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:86791000-86791200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr2:86791000-86791200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links