Variant report

Variant	rs11672000
Chromosome Location	chr19:55690751-55690752
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	POLR2A	chr19:55690749-55690863	ProgFib	skin:	n/a	n/a
2	BRCA1	chr19:55690549-55690945	GM12878	blood:	n/a	n/a
3	ZC3H11A	chr19:55690408-55690818	K562	blood:	n/a	n/a
4	HCFC1	chr19:55690088-55690969	K562	blood:	n/a	n/a
5	JUND	chr19:55690090-55690906	A549	lung:	n/a	chr19:55690279-55690293
6	SIN3AK20	chr19:55690575-55691134	A549	lung:	n/a	n/a
7	NR2F2	chr19:55690384-55691183	K562	blood:	n/a	n/a
8	GABPA	chr19:55690140-55690900	K562	blood:	n/a	n/a
9	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
10	JUN	chr19:55689997-55692239	K562	blood:	n/a	chr19:55690959-55690968 chr19:55690279-55690293
11	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
12	MAFK	chr19:55690458-55690846	K562	blood:	n/a	n/a
13	CREB1	chr19:55690031-55691002	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBL1XR1	chr19:55690248-55690972	K562	blood:	n/a	n/a
15	EBF1	chr19:55690547-55691014	GM12878	blood:	n/a	n/a
16	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
17	ELF1	chr19:55690194-55690960	K562	blood:	n/a	chr19:55690718-55690727
18	FOXP2	chr19:55690420-55690985	PFSK-1	brain:	n/a	n/a
19	CHD2	chr19:55690332-55691015	K562	blood:	n/a	chr19:55690694-55690704
20	SIX5	chr19:55690325-55690943	K562	blood:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
21	CHD2	chr19:55690183-55690832	HepG2	liver:	n/a	chr19:55690694-55690704
22	RCOR1	chr19:55690568-55691126	K562	blood:	n/a	n/a
23	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
24	SIN3AK20	chr19:55690648-55691885	PANC-1	pancreas:	n/a	n/a
25	GABPA	chr19:55690470-55690779	HepG2	liver:	n/a	n/a
26	THAP1	chr19:55690596-55691002	K562	blood:	n/a	n/a
27	RUNX3	chr19:55690341-55691041	GM12878	blood:	n/a	n/a
28	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
29	REST	chr19:55690154-55691223	SK-N-SH	brain:	n/a	n/a
30	ELF1	chr19:55690380-55690859	HepG2	liver:	n/a	chr19:55690718-55690727
31	NFATC1	chr19:55690488-55690863	GM12878	blood:	n/a	n/a
32	ATF3	chr19:55690446-55691005	A549	lung:	n/a	chr19:55690849-55690863
33	EGR1	chr19:55690134-55690850	K562	blood:	n/a	chr19:55690507-55690531 chr19:55690565-55690589
34	ELK1	chr19:55690410-55691031	GM12878	blood:	n/a	chr19:55690719-55690728 chr19:55690719-55690728
35	POLR2A	chr19:55690065-55692089	H1-neurons	neurons:	n/a	n/a
36	MAZ	chr19:55690105-55691151	HepG2	liver:	n/a	n/a
37	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
38	TAF1	chr19:55690154-55691948	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr19:55690355-55690963	U87	brain:	n/a	n/a
40	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
41	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
42	MAX	chr19:55690461-55690932	GM12878	blood:	n/a	n/a
43	SIN3A	chr19:55690044-55691845	H1-hESC	embryonic stem cell:	n/a	chr19:55691573-55691587 chr19:55691577-55691586 chr19:55691568-55691581 chr19:55691592-55691605
44	SIX5	chr19:55690243-55690822	GM12878	blood:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
45	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
46	ZBTB7A	chr19:55690602-55690865	K562	blood:	n/a	n/a
47	RUNX3	chr19:55690298-55690969	GM12878	blood:	n/a	n/a
48	FOSL2	chr19:55690212-55690786	A549	lung:	n/a	chr19:55690279-55690293
49	CUX1	chr19:55690495-55691009	GM12878	blood:	n/a	n/a
50	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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55690741-55690791	SK-N-MC	brain:	n/a
2	chr19:55690741-55690791	SK-N-SH	brain:	n/a
3	chr19:55690741-55690791	GM12892	blood:	n/a
4	chr19:55690741-55690791	AoSMC	blood vessel:	n/a
5	chr19:55690741-55690791	NH-A	brain:	n/a
6	chr19:55690741-55690791	AG09309	skin:	n/a
7	chr19:55690741-55690791	SKMC	muscle:	n/a
8	chr19:55690741-55690791	AG04450	lung:	fetal
9	chr19:55690741-55690791	HUVEC	blood vessel:	n/a
10	chr19:55690741-55690791	AG04449	skin:	fetal
11	chr19:55690741-55690791	PrEC	prostate:	n/a
12	chr19:55690741-55690791	IMR90	lung:	fetal
13	chr19:55690741-55690791	T-47D	breast:	n/a
14	chr19:55690741-55690791	NHDF-neo	bronchial:	n/a
15	chr19:55690741-55690791	HepG2	liver:	n/a
16	chr19:55690741-55690791	NHBE	bronchial:	n/a
17	chr19:55690741-55690791	PFSK-1	brain:	n/a
18	chr19:55690741-55690791	HMEC	breast:	n/a
19	chr19:55690741-55690791	HPAEpiC	pulmonary alveolar:	n/a
20	chr19:55690741-55690791	AG09319	gingival:	n/a
21	chr19:55690741-55690791	ProgFib	skin:	n/a
22	chr19:55690741-55690791	PANC-1	pancreas:	n/a
23	chr19:55690741-55690791	HRCEpiC	kidney:	n/a
24	chr19:55690741-55690791	NB4	blood:	n/a
25	chr19:55690741-55690791	HCF	heart:	n/a
26	chr19:55690741-55690791	Jurkat	blood:	n/a
27	chr19:55690741-55690791	LNCaP	prostate:	n/a
28	chr19:55690741-55690791	GM06990	blood:	n/a
29	chr19:55690741-55690791	HRPEpiC	eye:	n/a
30	chr19:55690741-55690791	HNPCEpiC	eye:	n/a
31	chr19:55690741-55690791	HIPEpiC	eye:	n/a
32	chr19:55690741-55690791	Hepatocyte	liver:	n/a
33	chr19:55690741-55690791	HL-60	blood:	n/a
34	chr19:55690741-55690791	BE2_C	brain:	n/a
35	chr19:55690741-55690791	Caco-2	colon:	n/a
36	chr19:55690741-55690791	MCF-7	breast:	n/a
37	chr19:55690741-55690791	HRE	kidney:	n/a
38	chr19:55690741-55690791	ECC-1	luminal epithelium:	n/a
39	chr19:55690741-55690791	A549	lung:	n/a
40	chr19:55690741-55690791	K562	blood:	n/a
41	chr19:55690741-55690791	GM19239	blood:	n/a
42	chr19:55690741-55690791	MCF10A-Er-Src	breast:	n/a
43	chr19:55690741-55690791	BJ	skin:	n/a
44	chr19:55690741-55690791	ovcar-3	ovarian:	n/a
45	chr19:55690741-55690791	SAEC	small airway:	n/a
46	chr19:55690741-55690791	HEK293	kidney:	embryo
47	chr19:55690741-55690791	AG10803	skin:	n/a
48	chr19:55690741-55690791	HCM	heart:	n/a
49	chr19:55690741-55690791	SK-N-SH_RA	brain:	n/a
50	chr19:55690741-55690791	NT2-D1	testis:	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	chr19:55690523..55693470-chr19:55767618..55771014,3	K562	blood:
4	chr19:55688939..55693251-chr19:55917287..55920595,8	K562	blood:
5	chr19:55689704..55692023-chr19:55769514..55771598,2	K562	blood:
6	chr19:55690071..55692651-chr19:55739628..55742521,2	MCF-7	breast:
7	chr19:55688567..55692973-chr19:55725028..55730023,9	K562	blood:
8	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
9	chr19:55689066..55691659-chr19:55726623..55728296,2	MCF-7	breast:
10	chr19:55688770..55691626-chr19:55917418..55920191,3	K562	blood:
11	chr19:55690189..55693086-chr19:55769247..55770801,2	MCF-7	breast:
12	chr19:55690042..55692776-chr19:55717237..55718780,2	K562	blood:
13	chr19:55688544..55691824-chr19:55726439..55729589,6	K562	blood:

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10424638	0.88[ASN][1000 genomes]
rs11669300	1.00[ASN][1000 genomes]
rs11670538	0.84[ASN][1000 genomes]
rs11671671	0.92[ASN][1000 genomes]
rs11672834	1.00[ASN][1000 genomes]
rs16986289	0.88[ASN][1000 genomes]
rs16986292	0.88[ASN][1000 genomes]
rs16986294	0.88[ASN][1000 genomes]
rs3729837	0.88[ASN][1000 genomes]
rs3729841	0.88[ASN][1000 genomes]
rs3859540	0.88[ASN][1000 genomes]
rs3859542	0.88[ASN][1000 genomes]
rs6509927	0.88[ASN][1000 genomes]
rs6509930	0.84[ASN][1000 genomes]
rs7248799	0.88[ASN][1000 genomes]
rs8107129	0.84[ASN][1000 genomes]
rs8107736	0.84[ASN][1000 genomes]
rs9749340	0.84[ASN][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:125 , 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	chr19:55689800-55690800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:55689800-55691000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:55689800-55691000	Active TSS	Brain Cingulate Gyrus	brain
6	chr19:55690000-55690800	Flanking Active TSS	Dnd41	blood
7	chr19:55690000-55691000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:55690000-55691000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr19:55690000-55691000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:55690000-55691000	Active TSS	Fetal Brain Female	brain
11	chr19:55690000-55691200	Active TSS	HepG2	liver
12	chr19:55690000-55691400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:55690000-55691600	Active TSS	Brain Anterior Caudate	brain
14	chr19:55690200-55690800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
15	chr19:55690200-55690800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
16	chr19:55690200-55691000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:55690200-55691000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:55690200-55691000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:55690200-55691000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:55690200-55691000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr19:55690200-55691000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:55690200-55691000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr19:55690200-55691000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
24	chr19:55690200-55691200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:55690200-55691200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
26	chr19:55690200-55691200	Flanking Active TSS	GM12878-XiMat	blood
27	chr19:55690200-55691400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:55690200-55691400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
29	chr19:55690200-55691400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
30	chr19:55690200-55691400	Bivalent Enhancer	Ovary	ovary
31	chr19:55690200-55691600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr19:55690200-55691600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr19:55690200-55691600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr19:55690200-55691600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:55690200-55691600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr19:55690200-55691600	Flanking Bivalent TSS/Enh	Thymus	Thymus
37	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
38	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:55690200-55691800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
41	chr19:55690200-55691800	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr19:55690200-55692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr19:55690200-55692000	Bivalent Enhancer	Placenta	Placenta
44	chr19:55690200-55692200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:55690400-55690800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:55690400-55690800	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr19:55690400-55690800	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
48	chr19:55690400-55690800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
49	chr19:55690400-55690800	Active TSS	NHDF-Ad	bronchial
50	chr19:55690400-55690800	Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links