Variant report

Variant	rs2619363
Chromosome Location	chr4:90759047-90759048
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr4:90757293-90759857	H1-neurons	neurons:	n/a	chr4:90758798-90758811 chr4:90758722-90758742 chr4:90758722-90758742 chr4:90757347-90757360 chr4:90758747-90758760 chr4:90758202-90758215
2	CTCF	chr4:90758900-90759050	GM12864	blood:	n/a	n/a
3	POLR2A	chr4:90757941-90759580	H1-neurons	neurons:	n/a	n/a
4	MAX	chr4:90757982-90759110	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
5	POLR2A	chr4:90758068-90759085	HEK293	kidney:	n/a	n/a
6	GATA2	chr4:90757246-90759504	SH-SY5Y	brain:	n/a	chr4:90758439-90758447 chr4:90758097-90758105
7	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr4:90757959-90759244	HUVEC	blood vessel:	n/a	n/a
9	TBP	chr4:90757998-90759047	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:90757883-90759635	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr4:90757892-90759167	HUVEC	blood vessel:	n/a	n/a
12	MYC	chr4:90758475-90759059	H1-hESC	embryonic stem cell:	n/a	n/a
13	STAT3	chr4:90758992-90759417	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr4:90758749-90759199	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr4:90758927-90759056	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr4:90757970-90759061	PBDE	blood:	n/a	n/a
17	SIN3A	chr4:90757284-90759458	H1-hESC	embryonic stem cell:	n/a	chr4:90759043-90759052
18	RAD21	chr4:90758566-90759098	H1-hESC	embryonic stem cell:	n/a	chr4:90758776-90758790
19	KAP1	chr4:90758735-90759542	HEK293	kidney:	n/a	n/a
20	CTCF	chr4:90758980-90759130	GM12873	blood:	n/a	n/a
21	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
22	GATA1	chr4:90758615-90760183	PBDE	blood:	n/a	n/a
23	CTCF	chr4:90758900-90759050	HEEpiC	esophagus:	n/a	n/a
24	POLR2A	chr4:90757921-90759119	H1-hESC	embryonic stem cell:	n/a	n/a
25	KAP1	chr4:90758738-90759409	U2OS	brain:	n/a	n/a
26	POLR2A	chr4:90757983-90759083	MCF10A-Er-Src	breast:	n/a	n/a
27	ZNF263	chr4:90757362-90759526	HEK293-T-REx	kidney:	n/a	chr4:90757923-90757932
28	STAT3	chr4:90758976-90759152	MCF10A-Er-Src	breast:	n/a	n/a
29	RCOR1	chr4:90758674-90759375	K562	blood:	n/a	n/a
30	CTCF	chr4:90758920-90759070	BE2_C	brain:	n/a	n/a
31	RAD21	chr4:90758655-90759058	SK-N-SH_RA	brain:	n/a	chr4:90758776-90758790

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:90759046-90759096	GM19239	blood:	n/a
2	chr4:90759046-90759096	NT2-D1	testis:	n/a
3	chr4:90759046-90759096	K562	blood:	n/a
4	chr4:90759046-90759096	HL-60	blood:	n/a
5	chr4:90759046-90759096	AG09319	gingival:	n/a
6	chr4:90759046-90759096	MCF-7	breast:	n/a
7	chr4:90759046-90759096	HRCEpiC	kidney:	n/a
8	chr4:90759046-90759096	HCM	heart:	n/a
9	chr4:90759046-90759096	GM12892	blood:	n/a
10	chr4:90759046-90759096	ECC-1	luminal epithelium:	n/a
11	chr4:90759046-90759096	U87	brain:	n/a
12	chr4:90759046-90759096	BJ	skin:	n/a
13	chr4:90759046-90759096	AG09309	skin:	n/a
14	chr4:90759046-90759096	HCT-116	colon:	n/a
15	chr4:90759046-90759096	LNCaP	prostate:	n/a
16	chr4:90759046-90759096	HCF	heart:	n/a
17	chr4:90759046-90759096	Hepatocyte	liver:	n/a
18	chr4:90759046-90759096	PFSK-1	brain:	n/a
19	chr4:90759046-90759096	HepG2	liver:	n/a
20	chr4:90759046-90759096	AG10803	skin:	n/a
21	chr4:90759046-90759096	HNPCEpiC	eye:	n/a
22	chr4:90759046-90759096	HCPEpiC	choroid plexus:	n/a
23	chr4:90759046-90759096	A549	lung:	n/a
24	chr4:90759046-90759096	HAEpiC	amniotic membrane:	n/a
25	chr4:90759046-90759096	ProgFib	skin:	n/a
26	chr4:90759046-90759096	HEEpiC	esophagus:	n/a
27	chr4:90759046-90759096	NHBE	bronchial:	n/a
28	chr4:90759046-90759096	NHDF-neo	bronchial:	n/a
29	chr4:90759046-90759096	GM06990	blood:	n/a
30	chr4:90759046-90759096	SK-N-MC	brain:	n/a
31	chr4:90759046-90759096	NH-A	brain:	n/a
32	chr4:90759046-90759096	HUVEC	blood vessel:	n/a
33	chr4:90759046-90759096	HRE	kidney:	n/a
34	chr4:90759046-90759096	BE2_C	brain:	n/a
35	chr4:90759046-90759096	MCF10A-Er-Src	breast:	n/a
36	chr4:90759046-90759096	HMEC	breast:	n/a
37	chr4:90759046-90759096	Hela-S3	cervix:	n/a
38	chr4:90759046-90759096	IMR90	lung:	fetal
39	chr4:90759046-90759096	SK-N-SH	brain:	n/a
40	chr4:90759046-90759096	RPTEC	kidney:	n/a
41	chr4:90759046-90759096	NB4	blood:	n/a
42	chr4:90759046-90759096	AoSMC	blood vessel:	n/a
43	chr4:90759046-90759096	HIPEpiC	eye:	n/a
44	chr4:90759046-90759096	Caco-2	colon:	n/a
45	chr4:90759046-90759096	HPAEpiC	pulmonary alveolar:	n/a
46	chr4:90759046-90759096	PANC-1	pancreas:	n/a
47	chr4:90759046-90759096	AG04449	skin:	fetal
48	chr4:90759046-90759096	HRPEpiC	eye:	n/a
49	chr4:90759046-90759096	GM12891	blood:	n/a
50	chr4:90759046-90759096	SKMC	muscle:	n/a

No data

Variant related genes	Relation type
SNCA	TF binding region
SNCA	CpG island

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs13142587	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1372516	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1442146	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1442147	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1442149	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2028535	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2165614	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2583958	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2583959	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2583965	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2583966	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2583967	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2583969	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583970	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583971	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583973	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583974	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583976	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583977	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583980	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583981	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583982	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583983	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583984	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583985	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583987	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2583988	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2583989	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2619343	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2619344	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2619345	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2619346	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2619348	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2619350	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619351	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619352	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619353	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619354	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619358	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619359	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619360	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619361	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619362	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619364	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619366	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2619367	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2619370	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2619371	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2619373	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2736995	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2736996	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736997	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736998	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736999	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737000	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737001	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737003	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737004	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737005	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737006	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737008	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737009	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737012	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737013	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737014	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737015	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737016	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737017	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737018	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2737019	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2737022	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2737023	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2737024	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2737033	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2737035	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs33965306	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs356163	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356184	0.85[EUR][1000 genomes]
rs356185	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs356187	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356189	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356192	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356195	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356199	0.84[EUR][1000 genomes]
rs67876224	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs986609	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs986610	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs990086	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs990087	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs990088	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90755600-90759800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:90755800-90759600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:90755800-90759600	Active TSS	Fetal Brain Female	brain
4	chr4:90756600-90759400	Active TSS	Brain Anterior Caudate	brain
5	chr4:90756600-90759600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr4:90756800-90759600	Active TSS	Ovary	ovary
7	chr4:90756800-90759800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr4:90757000-90759400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:90757000-90759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:90757000-90759600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:90757200-90759400	Active TSS	Brain Hippocampus Middle	brain
12	chr4:90757200-90759600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:90757200-90759600	Active TSS	Brain Cingulate Gyrus	brain
14	chr4:90757200-90759800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:90757400-90759400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
16	chr4:90757400-90759400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
17	chr4:90757400-90759400	Active TSS	Right Atrium	heart
18	chr4:90757400-90759600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:90757400-90759600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:90757400-90759600	Active TSS	Brain Angular Gyrus	brain
21	chr4:90757400-90759600	Active TSS	Fetal Brain Male	brain
22	chr4:90757400-90760200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:90757600-90759200	Bivalent/Poised TSS	Left Ventricle	heart
24	chr4:90757600-90759400	Bivalent/Poised TSS	Esophagus	oesophagus
25	chr4:90757600-90759400	Active TSS	K562	blood
26	chr4:90757600-90759600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:90757800-90759200	Active TSS	Fetal Lung	lung
28	chr4:90757800-90759400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:90757800-90759400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:90757800-90759400	Active TSS	Lung	lung
31	chr4:90757800-90759600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr4:90757800-90759600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:90757800-90759600	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr4:90757800-90759600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:90757800-90759800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr4:90758000-90759200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
37	chr4:90758000-90759200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
38	chr4:90758000-90759600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr4:90758000-90759600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:90758000-90759800	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr4:90758200-90759200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:90758200-90759200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:90758200-90759200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:90758200-90759200	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:90758200-90759200	Active TSS	Aorta	Aorta
46	chr4:90758200-90759200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
47	chr4:90758200-90759400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:90758200-90759600	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr4:90758200-90759600	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr4:90758200-90759800	Active TSS	ES-I3 Cell Line	embryonic stem cell

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