Variant report

Variant	rs11672834
Chromosome Location	chr19:55690890-55690891
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	BRCA1	chr19:55690549-55690945	GM12878	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	SIN3AK20	chr19:55690575-55691134	A549	lung:	n/a	n/a
5	NR2F2	chr19:55690384-55691183	K562	blood:	n/a	n/a
6	GABPA	chr19:55690140-55690900	K562	blood:	n/a	n/a
7	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
8	JUN	chr19:55689997-55692239	K562	blood:	n/a	chr19:55690959-55690968 chr19:55690279-55690293
9	CREB1	chr19:55690031-55691002	H1-hESC	embryonic stem cell:	n/a	n/a
10	TBL1XR1	chr19:55690248-55690972	K562	blood:	n/a	n/a
11	EBF1	chr19:55690547-55691014	GM12878	blood:	n/a	n/a
12	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
13	ELF1	chr19:55690194-55690960	K562	blood:	n/a	chr19:55690718-55690727
14	FOXP2	chr19:55690420-55690985	PFSK-1	brain:	n/a	n/a
15	CHD2	chr19:55690332-55691015	K562	blood:	n/a	chr19:55690694-55690704
16	SIX5	chr19:55690325-55690943	K562	blood:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
17	RCOR1	chr19:55690568-55691126	K562	blood:	n/a	n/a
18	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
19	SIN3AK20	chr19:55690648-55691885	PANC-1	pancreas:	n/a	n/a
20	THAP1	chr19:55690596-55691002	K562	blood:	n/a	n/a
21	RUNX3	chr19:55690341-55691041	GM12878	blood:	n/a	n/a
22	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
23	REST	chr19:55690154-55691223	SK-N-SH	brain:	n/a	n/a
24	ATF3	chr19:55690446-55691005	A549	lung:	n/a	chr19:55690849-55690863
25	ELK1	chr19:55690410-55691031	GM12878	blood:	n/a	chr19:55690719-55690728 chr19:55690719-55690728
26	POLR2A	chr19:55690065-55692089	H1-neurons	neurons:	n/a	n/a
27	MAZ	chr19:55690105-55691151	HepG2	liver:	n/a	n/a
28	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
29	TAF1	chr19:55690154-55691948	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr19:55690355-55690963	U87	brain:	n/a	n/a
31	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
32	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
33	MAX	chr19:55690461-55690932	GM12878	blood:	n/a	n/a
34	SIN3A	chr19:55690044-55691845	H1-hESC	embryonic stem cell:	n/a	chr19:55691573-55691587 chr19:55691577-55691586 chr19:55691568-55691581 chr19:55691592-55691605
35	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
36	RUNX3	chr19:55690298-55690969	GM12878	blood:	n/a	n/a
37	CUX1	chr19:55690495-55691009	GM12878	blood:	n/a	n/a
38	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
39	CHD2	chr19:55689989-55690890	H1-hESC	embryonic stem cell:	n/a	chr19:55690694-55690704
40	SIX5	chr19:55689962-55691205	A549	lung:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
41	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
42	PAX5	chr19:55690591-55691028	GM12892	blood:	n/a	n/a
43	RELA	chr19:55690445-55691005	GM18951	blood:	n/a	n/a
44	POU2F2	chr19:55690429-55690987	GM12878	blood:	n/a	chr19:55690956-55690968
45	EBF1	chr19:55690422-55691111	GM12878	blood:	n/a	n/a
46	MAX	chr19:55690468-55691033	ECC-1	luminal epithelium:	n/a	n/a
47	GABPA	chr19:55690105-55690993	K562	blood:	n/a	n/a
48	RCOR1	chr19:55690192-55691063	GM12878	blood:	n/a	n/a
49	ATF3	chr19:55690310-55690903	K562	blood:	n/a	chr19:55690849-55690863
50	BHLHE40	chr19:55690511-55691930	K562	blood:	n/a	chr19:55691570-55691586

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55690876-55690926	GM12891	blood:	n/a
2	chr19:55690876-55690926	NB4	blood:	n/a
3	chr19:55690876-55690926	AG04450	lung:	fetal
4	chr19:55690876-55690926	GM12878	blood:	n/a
5	chr19:55690876-55690926	AG09309	skin:	n/a
6	chr19:55690876-55690926	U87	brain:	n/a
7	chr19:55690876-55690926	BE2_C	brain:	n/a
8	chr19:55690876-55690926	H1-hESC	embryonic stem cell:	embryo
9	chr19:55690876-55690926	ProgFib	skin:	n/a
10	chr19:55690876-55690926	SAEC	small airway:	n/a
11	chr19:55690876-55690926	ovcar-3	ovarian:	n/a
12	chr19:55690876-55690926	Hepatocyte	liver:	n/a
13	chr19:55690876-55690926	HCF	heart:	n/a
14	chr19:55690876-55690926	A549	lung:	n/a
15	chr19:55690876-55690926	AG04449	skin:	fetal
16	chr19:55690876-55690926	HAEpiC	amniotic membrane:	n/a
17	chr19:55690876-55690926	PFSK-1	brain:	n/a
18	chr19:55690876-55690926	T-47D	breast:	n/a
19	chr19:55690876-55690926	NH-A	brain:	n/a
20	chr19:55690876-55690926	SK-N-SH_RA	brain:	n/a
21	chr19:55690876-55690926	K562	blood:	n/a
22	chr19:55690876-55690926	SK-N-MC	brain:	n/a
23	chr19:55690876-55690926	HL-60	blood:	n/a
24	chr19:55690876-55690926	NHDF-neo	bronchial:	n/a
25	chr19:55690876-55690926	HepG2	liver:	n/a
26	chr19:55690876-55690926	MCF10A-Er-Src	breast:	n/a
27	chr19:55690876-55690926	PrEC	prostate:	n/a
28	chr19:55690876-55690926	HMEC	breast:	n/a
29	chr19:55690876-55690926	HUVEC	blood vessel:	n/a
30	chr19:55690876-55690926	AG09319	gingival:	n/a
31	chr19:55690876-55690926	GM06990	blood:	n/a
32	chr19:55690876-55690926	Caco-2	colon:	n/a
33	chr19:55690876-55690926	CMK	blood:	n/a
34	chr19:55690876-55690926	GM19239	blood:	n/a
35	chr19:55690876-55690926	RPTEC	kidney:	n/a
36	chr19:55690876-55690926	Jurkat	blood:	n/a
37	chr19:55690876-55690926	SKMC	muscle:	n/a
38	chr19:55690876-55690926	ECC-1	luminal epithelium:	n/a
39	chr19:55690876-55690926	HRCEpiC	kidney:	n/a
40	chr19:55690876-55690926	HIPEpiC	eye:	n/a
41	chr19:55690876-55690926	SK-N-SH	brain:	n/a
42	chr19:55690876-55690926	HEK293	kidney:	embryo
43	chr19:55690876-55690926	HNPCEpiC	eye:	n/a
44	chr19:55690876-55690926	HCM	heart:	n/a
45	chr19:55690876-55690926	MCF-7	breast:	n/a
46	chr19:55690876-55690926	AG10803	skin:	n/a
47	chr19:55690876-55690926	LNCaP	prostate:	n/a
48	chr19:55690876-55690926	HRPEpiC	eye:	n/a
49	chr19:55690876-55690926	NHBE	bronchial:	n/a
50	chr19:55690876-55690926	IMR90	lung:	fetal

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
ENSG00000267265	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000180089	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10424638	0.88[ASN][1000 genomes]
rs11669300	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670538	0.84[ASN][1000 genomes]
rs11671671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11672000	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]
rs61735060	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][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:124 , 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	chr19:55689800-55691000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:55689800-55691000	Active TSS	Brain Cingulate Gyrus	brain
5	chr19:55690000-55691000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:55690000-55691000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr19:55690000-55691000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:55690000-55691000	Active TSS	Fetal Brain Female	brain
9	chr19:55690000-55691200	Active TSS	HepG2	liver
10	chr19:55690000-55691400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:55690000-55691600	Active TSS	Brain Anterior Caudate	brain
12	chr19:55690200-55691000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:55690200-55691000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:55690200-55691000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr19:55690200-55691000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:55690200-55691000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr19:55690200-55691000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:55690200-55691000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
19	chr19:55690200-55691000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
20	chr19:55690200-55691200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:55690200-55691200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
22	chr19:55690200-55691200	Flanking Active TSS	GM12878-XiMat	blood
23	chr19:55690200-55691400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:55690200-55691400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr19:55690200-55691400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
26	chr19:55690200-55691400	Bivalent Enhancer	Ovary	ovary
27	chr19:55690200-55691600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr19:55690200-55691600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr19:55690200-55691600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr19:55690200-55691600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:55690200-55691600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
32	chr19:55690200-55691600	Flanking Bivalent TSS/Enh	Thymus	Thymus
33	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:55690200-55691800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
37	chr19:55690200-55691800	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr19:55690200-55692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr19:55690200-55692000	Bivalent Enhancer	Placenta	Placenta
40	chr19:55690200-55692200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:55690400-55691000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:55690400-55691000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr19:55690400-55691000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
44	chr19:55690400-55691000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
45	chr19:55690400-55691000	Transcr. at gene 5' and 3'	Right Atrium	heart
46	chr19:55690400-55691000	Flanking Active TSS	Right Ventricle	heart
47	chr19:55690400-55691000	Flanking Active TSS	A549	lung
48	chr19:55690400-55691200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:55690400-55691200	Bivalent Enhancer	Liver	Liver
50	chr19:55690400-55691200	Bivalent/Poised TSS	Fetal Kidney	kidney

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