Variant report

Variant	rs2301278
Chromosome Location	chr19:55690424-55690425
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	ZC3H11A	chr19:55690408-55690818	K562	blood:	n/a	n/a
2	HCFC1	chr19:55690088-55690969	K562	blood:	n/a	n/a
3	JUND	chr19:55690090-55690906	A549	lung:	n/a	chr19:55690279-55690293
4	NR2F2	chr19:55690384-55691183	K562	blood:	n/a	n/a
5	TEAD4	chr19:55690121-55690499	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr19:55690140-55690900	K562	blood:	n/a	n/a
7	YY1	chr19:55690061-55690744	GM12878	blood:	n/a	n/a
8	SP1	chr19:55689984-55690977	GM12878	blood:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690845-55690854 chr19:55690307-55690317 chr19:55690843-55690855 chr19:55690701-55690714
9	JUN	chr19:55689997-55692239	K562	blood:	n/a	chr19:55690959-55690968 chr19:55690279-55690293
10	ETS1	chr19:55690283-55690875	GM12878	blood:	n/a	chr19:55690719-55690728 chr19:55690719-55690728 chr19:55690720-55690730 chr19:55690576-55690589 chr19:55690578-55690585 chr19:55690719-55690730 chr19:55690507-55690520 chr19:55690719-55690728 chr19:55690717-55690726 chr19:55690719-55690728 chr19:55690718-55690727 chr19:55690716-55690729 chr19:55690719-55690728 chr19:55690719-55690728 chr19:55690506-55690519
11	CREB1	chr19:55690031-55691002	H1-hESC	embryonic stem cell:	n/a	n/a
12	TBL1XR1	chr19:55690248-55690972	K562	blood:	n/a	n/a
13	REST	chr19:55690386-55692323	PFSK-1	brain:	n/a	chr19:55691568-55691588 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
14	ELF1	chr19:55690194-55690960	K562	blood:	n/a	chr19:55690718-55690727
15	TAF1	chr19:55690124-55690658	H1-neurons	neurons:	n/a	n/a
16	CREB1	chr19:55690407-55690611	A549	lung:	n/a	n/a
17	FOXP2	chr19:55690420-55690985	PFSK-1	brain:	n/a	n/a
18	CHD2	chr19:55690332-55691015	K562	blood:	n/a	chr19:55690694-55690704
19	SIX5	chr19:55690325-55690943	K562	blood:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
20	CHD2	chr19:55690183-55690832	HepG2	liver:	n/a	chr19:55690694-55690704
21	SP1	chr19:55689974-55690973	GM12878	blood:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690845-55690854 chr19:55690307-55690317 chr19:55690843-55690855 chr19:55690701-55690714
22	RUNX3	chr19:55690341-55691041	GM12878	blood:	n/a	n/a
23	REST	chr19:55690261-55692603	PANC-1	pancreas:	n/a	chr19:55691568-55691588 chr19:55692420-55692429 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
24	REST	chr19:55690154-55691223	SK-N-SH	brain:	n/a	n/a
25	EP300	chr19:55690046-55690431	H1-hESC	embryonic stem cell:	n/a	n/a
26	YY1	chr19:55690062-55690607	H1-hESC	embryonic stem cell:	n/a	n/a
27	ELF1	chr19:55690380-55690859	HepG2	liver:	n/a	chr19:55690718-55690727
28	EGR1	chr19:55690134-55690850	K562	blood:	n/a	chr19:55690507-55690531 chr19:55690565-55690589
29	ELK1	chr19:55690410-55691031	GM12878	blood:	n/a	chr19:55690719-55690728 chr19:55690719-55690728
30	POLR2A	chr19:55690065-55692089	H1-neurons	neurons:	n/a	n/a
31	MAZ	chr19:55690105-55691151	HepG2	liver:	n/a	n/a
32	ZNF143	chr19:55690221-55690971	GM12878	blood:	n/a	chr19:55690508-55690526 chr19:55690577-55690586 chr19:55690655-55690673 chr19:55690570-55690588 chr19:55690512-55690531 chr19:55690579-55690588 chr19:55690410-55690428
33	TAF1	chr19:55690154-55691948	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr19:55690355-55690963	U87	brain:	n/a	n/a
35	REST	chr19:55690082-55692299	A549	lung:	n/a	chr19:55691568-55691588 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
36	REST	chr19:55690169-55692215	SK-N-SH	brain:	n/a	chr19:55691568-55691588 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
37	SIN3A	chr19:55690044-55691845	H1-hESC	embryonic stem cell:	n/a	chr19:55691573-55691587 chr19:55691577-55691586 chr19:55691568-55691581 chr19:55691592-55691605
38	SIX5	chr19:55690243-55690822	GM12878	blood:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
39	REST	chr19:55690331-55692312	U87	brain:	n/a	chr19:55691568-55691588 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
40	ZNF143	chr19:55690414-55690707	Hela-S3	cervix:	n/a	chr19:55690508-55690526 chr19:55690577-55690586 chr19:55690655-55690673 chr19:55690570-55690588 chr19:55690512-55690531 chr19:55690579-55690588
41	RUNX3	chr19:55690298-55690969	GM12878	blood:	n/a	n/a
42	FOSL2	chr19:55690212-55690786	A549	lung:	n/a	chr19:55690279-55690293
43	REST	chr19:55689830-55692121	H1-neurons	neurons:	n/a	chr19:55691568-55691588 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
44	TEAD4	chr19:55689974-55690425	HepG2	liver:	n/a	n/a
45	CHD2	chr19:55689989-55690890	H1-hESC	embryonic stem cell:	n/a	chr19:55690694-55690704
46	SIX5	chr19:55689962-55691205	A549	lung:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
47	SP1	chr19:55689929-55691037	A549	lung:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690845-55690854 chr19:55690307-55690317 chr19:55690843-55690855 chr19:55690701-55690714
48	SIX5	chr19:55690089-55690882	H1-hESC	embryonic stem cell:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
49	EBF1	chr19:55690422-55691111	GM12878	blood:	n/a	n/a
50	YY1	chr19:55690332-55690723	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55516495..55518136-chr19:55689009..55691049,2	K562	blood:
2	chr19:55688311..55691062-chr19:55894842..55896433,2	MCF-7	breast:
3	chr19:55688939..55693251-chr19:55917287..55920595,8	K562	blood:
4	chr19:55689704..55692023-chr19:55769514..55771598,2	K562	blood:
5	chr19:55690071..55692651-chr19:55739628..55742521,2	MCF-7	breast:
6	chr19:55688567..55692973-chr19:55725028..55730023,9	K562	blood:
7	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
8	chr19:55689066..55691659-chr19:55726623..55728296,2	MCF-7	breast:
9	chr19:55688770..55691626-chr19:55917418..55920191,3	K562	blood:
10	chr19:55690189..55693086-chr19:55769247..55770801,2	MCF-7	breast:
11	chr19:55690042..55692776-chr19:55717237..55718780,2	K562	blood:
12	chr19:55688544..55691824-chr19:55726439..55729589,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55689300-55690562	l_1714_chr19:55688749-55693967_brain

Variant related genes	Relation type
SYT5	TF binding region
ENSG00000267649	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000267265	Chromatin interaction
ENSG00000180089	Chromatin interaction
ENSG00000080031	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1128712	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12459688	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12459887	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12459917	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12459921	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12459930	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12460445	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12461148	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12461170	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12461195	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12461202	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12462211	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12463268	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17458	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071572	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071574	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2278281	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes]
rs2288420	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2288518	0.91[EUR][1000 genomes]
rs2288528	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes]
rs2288529	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes]
rs3745922	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3786867	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs3803903	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3826887	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3848618	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3859544	0.81[ASN][1000 genomes]
rs56666700	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56726774	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58017412	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58218194	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58824375	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59663064	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60176657	0.85[AMR][1000 genomes]
rs60799292	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61570139	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61704307	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7247152	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7247378	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7255625	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs8101500	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs890871	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9710458	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55689200-55691200	Enhancers	Primary hematopoietic stem cells	blood
2	chr19:55689200-55691200	Enhancers	Hela-S3	cervix
3	chr19:55689800-55690600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr19:55689800-55690800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr19:55689800-55691000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:55689800-55691000	Active TSS	Brain Cingulate Gyrus	brain
7	chr19:55690000-55690600	Active TSS	Primary T cells from cord blood	blood
8	chr19:55690000-55690600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:55690000-55690600	Bivalent Enhancer	Fetal Stomach	stomach
10	chr19:55690000-55690800	Flanking Active TSS	Dnd41	blood
11	chr19:55690000-55691000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:55690000-55691000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr19:55690000-55691000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:55690000-55691000	Active TSS	Fetal Brain Female	brain
15	chr19:55690000-55691200	Active TSS	HepG2	liver
16	chr19:55690000-55691400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:55690000-55691600	Active TSS	Brain Anterior Caudate	brain
18	chr19:55690200-55690600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr19:55690200-55690600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr19:55690200-55690600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:55690200-55690600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:55690200-55690600	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr19:55690200-55690600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr19:55690200-55690600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
25	chr19:55690200-55690600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
26	chr19:55690200-55690600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr19:55690200-55690600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:55690200-55690600	Flanking Active TSS	Brain Angular Gyrus	brain
29	chr19:55690200-55690600	Bivalent Enhancer	Spleen	Spleen
30	chr19:55690200-55690600	Enhancers	HMEC	breast
31	chr19:55690200-55690600	Active TSS	HSMM	muscle
32	chr19:55690200-55690600	Active TSS	Osteobl	bone
33	chr19:55690200-55690800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
34	chr19:55690200-55690800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
35	chr19:55690200-55691000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:55690200-55691000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:55690200-55691000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr19:55690200-55691000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:55690200-55691000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr19:55690200-55691000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:55690200-55691000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
42	chr19:55690200-55691000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr19:55690200-55691200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:55690200-55691200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
45	chr19:55690200-55691200	Flanking Active TSS	GM12878-XiMat	blood
46	chr19:55690200-55691400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr19:55690200-55691400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
48	chr19:55690200-55691400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
49	chr19:55690200-55691400	Bivalent Enhancer	Ovary	ovary
50	chr19:55690200-55691600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links