Variant report

Variant	rs55880062
Chromosome Location	chr1:161276014-161276015
allele	G/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	ZBTB7A	chr1:161275501-161276316	K562	blood:	n/a	chr1:161276109-161276116
2	BHLHE40	chr1:161276011-161276365	K562	blood:	n/a	n/a
3	YY1	chr1:161275842-161276254	HCT-116	colon:	n/a	chr1:161276089-161276100
4	CEBPB	chr1:161275743-161276105	K562	blood:	n/a	chr1:161275930-161275941
5	EP300	chr1:161275741-161276136	K562	blood:	n/a	n/a
6	UBTF	chr1:161275744-161276360	K562	blood:	n/a	n/a
7	SIN3A	chr1:161275182-161276354	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:161275687-161276246	NB4	blood:	n/a	n/a
9	POLR2A	chr1:161275757-161276067	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr1:161275812-161276098	HepG2	liver:	n/a	n/a
11	MXI1	chr1:161275313-161276513	SK-N-SH	brain:	n/a	n/a
12	MAX	chr1:161275581-161276387	K562	blood:	n/a	n/a
13	ZNF143	chr1:161275749-161276451	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:161275748-161276245	K562	blood:	n/a	n/a
15	CTCF	chr1:161275936-161276367	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:161275334-161276382	HL-60	blood:	n/a	n/a
17	YY1	chr1:161275823-161276315	K562	blood:	n/a	chr1:161276089-161276100
18	ELK1	chr1:161275944-161276116	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:161275761-161276138	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr1:161275843-161276167	K562	blood:	n/a	n/a
21	RUNX3	chr1:161275571-161276317	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:161275693-161276161	GM12878	blood:	n/a	n/a
23	IRF1	chr1:161275855-161276211	K562	blood:	n/a	chr1:161276102-161276116
24	MAZ	chr1:161275880-161276339	GM12878	blood:	n/a	n/a
25	HEY1	chr1:161275711-161276230	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:161275856-161276092	GM12891	blood:	n/a	n/a
27	POLR2A	chr1:161275745-161276229	GM18951	blood:	n/a	n/a
28	POLR2A	chr1:161275327-161276423	K562	blood:	n/a	n/a
29	SIN3AK20	chr1:161275356-161276028	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr1:161275670-161276398	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr1:161276000-161276350	Spleen_OC	spleen:	n/a	n/a
32	STAT5A	chr1:161275632-161276120	GM12878	blood:	n/a	chr1:161276085-161276097 chr1:161276083-161276095
33	WRNIP1	chr1:161275910-161276198	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:161275780-161276216	HUVEC	blood vessel:	n/a	n/a
35	MAZ	chr1:161275658-161276403	K562	blood:	n/a	n/a
36	GABPA	chr1:161275697-161276269	K562	blood:	n/a	n/a
37	POLR2A	chr1:161275762-161276191	GM19099	blood:	n/a	n/a
38	POLR2A	chr1:161275799-161276167	GM12892	blood:	n/a	n/a
39	NR2F2	chr1:161275634-161276608	K562	blood:	n/a	n/a
40	ELF1	chr1:161275245-161276405	GM12878	blood:	n/a	chr1:161276020-161276031
41	RFX5	chr1:161275935-161276161	GM12878	blood:	n/a	n/a
42	RAD21	chr1:161275992-161276351	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:161275786-161276319	K562	blood:	n/a	n/a
44	CTCF	chr1:161275958-161276361	K562	blood:	n/a	n/a
45	GABPA	chr1:161275678-161276152	HL-60	blood:	n/a	n/a
46	POLR2A	chr1:161275788-161276095	HepG2	liver:	n/a	n/a
47	RAD21	chr1:161275862-161276391	H1-hESC	embryonic stem cell:	n/a	n/a
48	SPI1	chr1:161275838-161276107	HL-60	blood:	n/a	chr1:161276021-161276028 chr1:161276020-161276029
49	CEBPB	chr1:161275807-161276085	HepG2	liver:	n/a	chr1:161275930-161275941
50	EGR1	chr1:161275864-161276205	K562	blood:	n/a	chr1:161276084-161276097

No.	Distal block	Cell Line	Cell type
1	chr1:161275235..161277911-chr1:161283525..161285261,2	MCF-7	breast:
2	chr1:161167464..161169651-chr1:161275959..161277953,2	K562	blood:
3	chr1:161192625..161198260-chr1:161274899..161278564,8	K562	blood:

Variant related genes	Relation type
MPZ	TF binding region
ENSG00000263548	Chromatin interaction
ENSG00000158859	Chromatin interaction
ENSG00000143252	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000158882	Chromatin interaction
ENSG00000158874	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs34887199	1.00[AMR][1000 genomes]
rs56758346	1.00[AMR][1000 genomes]
rs57560345	1.00[AMR][1000 genomes]
rs61642842	1.00[AMR][1000 genomes]
rs74124650	1.00[AMR][1000 genomes]
rs74124652	1.00[AMR][1000 genomes]
rs74124653	1.00[AMR][1000 genomes]
rs74124672	1.00[AMR][1000 genomes]
rs74124691	1.00[AMR][1000 genomes]
rs74124697	1.00[AMR][1000 genomes]
rs74124950	1.00[AMR][1000 genomes]
rs74127620	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv517826	chr1:161263380-161277601	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161273800-161276400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:161274200-161276200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr1:161274200-161276200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:161274200-161276200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr1:161274400-161276200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:161274400-161276200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:161274400-161276200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:161274400-161276200	Active TSS	GM12878-XiMat	blood
9	chr1:161274400-161276400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:161274400-161276400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:161274800-161276200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:161274800-161276200	Enhancers	Fetal Heart	heart
13	chr1:161274800-161276200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr1:161274800-161276400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr1:161274800-161276400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:161274800-161276400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:161274800-161276400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:161274800-161276600	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr1:161275000-161276200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:161275000-161276200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:161275000-161276200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:161275000-161276200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr1:161275000-161276200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:161275000-161276200	Flanking Active TSS	Colonic Mucosa	Colon
25	chr1:161275000-161276200	Active TSS	Rectal Smooth Muscle	rectum
26	chr1:161275000-161276400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr1:161275000-161276400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:161275000-161276400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:161275000-161276400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:161275000-161276400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:161275000-161276400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:161275200-161276200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:161275200-161276200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:161275200-161276200	Active TSS	Muscle Satellite Cultured Cells	--
35	chr1:161275200-161276200	Flanking Active TSS	Placenta	Placenta
36	chr1:161275200-161276200	Active TSS	Gastric	stomach
37	chr1:161275200-161276200	Active TSS	NHDF-Ad	bronchial
38	chr1:161275200-161276400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:161275200-161276400	Active TSS	Aorta	Aorta
40	chr1:161275200-161276400	Active TSS	Psoas Muscle	Psoas
41	chr1:161275200-161276600	Active TSS	Fetal Kidney	kidney
42	chr1:161275200-161277000	Active TSS	Colon Smooth Muscle	Colon
43	chr1:161275400-161276200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:161275400-161276200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:161275400-161276200	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:161275400-161276200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:161275400-161276200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:161275400-161276200	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr1:161275400-161276200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:161275400-161276200	Active TSS	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links