Variant report

Variant	rs3756063
Chromosome Location	chr4:90757394-90757395
allele	C/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	RCOR1	chr4:90757155-90757470	K562	blood:	n/a	n/a
2	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
3	GATA2	chr4:90757246-90759504	SH-SY5Y	brain:	n/a	chr4:90758439-90758447 chr4:90758097-90758105
4	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
5	EGR1	chr4:90757171-90757552	K562	blood:	n/a	chr4:90757343-90757356 chr4:90757342-90757357 chr4:90757344-90757353 chr4:90757343-90757356
6	HMGN3	chr4:90757259-90757513	K562	blood:	n/a	n/a
7	TAL1	chr4:90757184-90757567	K562	blood:	n/a	chr4:90757480-90757495 chr4:90757480-90757495 chr4:90757480-90757495
8	CCNT2	chr4:90757211-90757468	K562	blood:	n/a	n/a
9	CTCF	chr4:90757380-90757530	HUVEC	blood vessel:	n/a	n/a
10	EGR1	chr4:90757178-90757553	K562	blood:	n/a	chr4:90757343-90757356 chr4:90757342-90757357 chr4:90757344-90757353 chr4:90757343-90757356
11	E2F6	chr4:90757275-90758968	H1-hESC	embryonic stem cell:	n/a	chr4:90758514-90758521 chr4:90758510-90758522 chr4:90758514-90758521 chr4:90758464-90758473 chr4:90758511-90758525 chr4:90758514-90758521 chr4:90757373-90757383
12	SIN3A	chr4:90757284-90759458	H1-hESC	embryonic stem cell:	n/a	chr4:90759043-90759052
13	POLR2A	chr4:90757320-90757409	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr4:90756656-90757751	PBDE	blood:	n/a	n/a
15	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
16	ZNF263	chr4:90757349-90758919	K562	blood:	n/a	chr4:90757923-90757932
17	CTBP2	chr4:90757235-90758898	H1-hESC	embryonic stem cell:	n/a	n/a
18	GATA1	chr4:90756797-90758328	PBDE	blood:	n/a	chr4:90758097-90758105
19	ZNF263	chr4:90757362-90759526	HEK293-T-REx	kidney:	n/a	chr4:90757923-90757932

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:90757351-90757401	AG09319	gingival:	n/a
2	chr4:90757351-90757401	BJ	skin:	n/a
3	chr4:90757351-90757401	RPTEC	kidney:	n/a
4	chr4:90757351-90757401	Jurkat	blood:	n/a
5	chr4:90757378-90757428	HCPEpiC	choroid plexus:	n/a
6	chr4:90757378-90757428	PANC-1	pancreas:	n/a
7	chr4:90757351-90757401	AG09309	skin:	n/a
8	chr4:90757378-90757428	PrEC	prostate:	n/a
9	chr4:90757351-90757401	HMEC	breast:	n/a
10	chr4:90757378-90757428	HL-60	blood:	n/a
11	chr4:90757378-90757428	HRE	kidney:	n/a
12	chr4:90757351-90757401	AG04450	lung:	fetal
13	chr4:90757378-90757428	HEK293	kidney:	embryo
14	chr4:90757351-90757401	HCF	heart:	n/a
15	chr4:90757378-90757428	NHDF-neo	bronchial:	n/a
16	chr4:90757378-90757428	IMR90	lung:	fetal
17	chr4:90757378-90757428	K562	blood:	n/a
18	chr4:90757351-90757401	NT2-D1	testis:	n/a
19	chr4:90757378-90757428	MCF-7	breast:	n/a
20	chr4:90757378-90757428	CMK	blood:	n/a
21	chr4:90757378-90757428	SKMC	muscle:	n/a
22	chr4:90757378-90757428	HNPCEpiC	eye:	n/a
23	chr4:90757378-90757428	HRPEpiC	eye:	n/a
24	chr4:90757351-90757401	SKMC	muscle:	n/a
25	chr4:90757378-90757428	BJ	skin:	n/a
26	chr4:90757378-90757428	AG10803	skin:	n/a
27	chr4:90757351-90757401	HAEpiC	amniotic membrane:	n/a
28	chr4:90757351-90757401	ECC-1	luminal epithelium:	n/a
29	chr4:90757351-90757401	CMK	blood:	n/a
30	chr4:90757378-90757428	GM06990	blood:	n/a
31	chr4:90757378-90757428	HPAEpiC	pulmonary alveolar:	n/a
32	chr4:90757378-90757428	HEEpiC	esophagus:	n/a
33	chr4:90757351-90757401	NHDF-neo	bronchial:	n/a
34	chr4:90757351-90757401	SK-N-SH_RA	brain:	n/a
35	chr4:90757351-90757401	GM12891	blood:	n/a
36	chr4:90757378-90757428	HAEpiC	amniotic membrane:	n/a
37	chr4:90757378-90757428	ProgFib	skin:	n/a
38	chr4:90757351-90757401	AoSMC	blood vessel:	n/a
39	chr4:90757378-90757428	SK-N-MC	brain:	n/a
40	chr4:90757351-90757401	U87	brain:	n/a
41	chr4:90757378-90757428	GM12892	blood:	n/a
42	chr4:90757378-90757428	PFSK-1	brain:	n/a
43	chr4:90757378-90757428	AG04449	skin:	fetal
44	chr4:90757378-90757428	NB4	blood:	n/a
45	chr4:90757378-90757428	SK-N-SH	brain:	n/a
46	chr4:90757378-90757428	SAEC	small airway:	n/a
47	chr4:90757378-90757428	ovcar-3	ovarian:	n/a
48	chr4:90757351-90757401	AG04449	skin:	fetal
49	chr4:90757351-90757401	HEK293	kidney:	embryo
50	chr4:90757351-90757401	MCF10A-Er-Src	breast:	n/a

Variant related genes	Relation type
SNCA	TF binding region
ENSG00000247775	TF binding region
ENSG00000247775	CpG island
SNCA	CpG island

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10004413	0.90[EUR][1000 genomes]
rs10005233	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10008964	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10028246	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12331318	0.90[EUR][1000 genomes]
rs1348224	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1372517	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372518	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1372519	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1372520	1.00[ASN][1000 genomes]
rs1372521	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1372522	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1442135	0.81[EUR][1000 genomes]
rs1442140	0.81[EUR][1000 genomes]
rs1442144	0.83[ASN][1000 genomes]
rs1442148	0.86[ASN][1000 genomes]
rs1471483	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471484	1.00[ASN][1000 genomes]
rs1811442	0.86[ASN][1000 genomes]
rs1811443	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1822217	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1837891	0.83[ASN][1000 genomes]
rs184810	0.81[ASN][1000 genomes]
rs1899389	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2197120	0.83[ASN][1000 genomes]
rs2245801	0.91[ASN][1000 genomes]
rs2301134	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301135	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2572318	0.83[ASN][1000 genomes]
rs2572320	0.83[ASN][1000 genomes]
rs2583962	0.83[ASN][1000 genomes]
rs2583964	0.83[ASN][1000 genomes]
rs2583968	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2583972	0.86[ASN][1000 genomes]
rs2583975	0.86[ASN][1000 genomes]
rs2583978	0.98[ASN][1000 genomes]
rs2619341	0.83[ASN][1000 genomes]
rs2619347	0.84[ASN][1000 genomes]
rs2619349	0.86[ASN][1000 genomes]
rs2619355	0.86[ASN][1000 genomes]
rs2619356	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2619368	0.83[ASN][1000 genomes]
rs2737002	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2737010	0.82[ASN][1000 genomes]
rs2737011	0.86[ASN][1000 genomes]
rs2737021	0.83[ASN][1000 genomes]
rs2737025	0.83[ASN][1000 genomes]
rs2737028	0.83[ASN][1000 genomes]
rs2737030	0.83[ASN][1000 genomes]
rs28403500	0.90[EUR][1000 genomes]
rs28415623	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28507349	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28734152	0.90[EUR][1000 genomes]
rs28777703	0.90[EUR][1000 genomes]
rs3113355	0.84[ASN][1000 genomes]
rs35424815	0.90[EUR][1000 genomes]
rs356162	0.81[ASN][1000 genomes]
rs356186	0.83[ASN][1000 genomes]
rs3756059	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806789	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4293762	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58864428	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6532191	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532192	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6532193	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6816736	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6817001	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6828271	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6831847	0.83[EUR][1000 genomes]
rs6839608	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6843084	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6848181	0.82[EUR][1000 genomes]
rs748849	0.83[ASN][1000 genomes]
rs763443	0.80[EUR][1000 genomes]
rs7656954	0.83[EUR][1000 genomes]
rs7671549	0.90[EUR][1000 genomes]
rs7672979	0.90[EUR][1000 genomes]
rs7680557	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7680761	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7681154	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7681440	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687945	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7698219	0.90[EUR][1000 genomes]
rs894280	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs920624	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs990085	0.81[AFR][1000 genomes];1.00[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3756063	SNCA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90743400-90757400	Weak transcription	Gastric	stomach
2	chr4:90751400-90757400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:90755600-90759800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:90755800-90759600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:90755800-90759600	Active TSS	Fetal Brain Female	brain
6	chr4:90756200-90757400	Flanking Active TSS	Fetal Brain Male	brain
7	chr4:90756200-90757800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:90756400-90757400	Enhancers	Primary T cells from cord blood	blood
9	chr4:90756600-90757400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:90756600-90757400	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr4:90756600-90757400	Flanking Active TSS	HMEC	breast
12	chr4:90756600-90757600	Flanking Active TSS	HUVEC	blood vessel
13	chr4:90756600-90758000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:90756600-90758000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:90756600-90758600	Enhancers	Spleen	Spleen
16	chr4:90756600-90759000	Active TSS	Brain Substantia Nigra	brain
17	chr4:90756600-90759400	Active TSS	Brain Anterior Caudate	brain
18	chr4:90756600-90759600	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr4:90756800-90757400	Flanking Active TSS	NHEK	skin
20	chr4:90756800-90758000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:90756800-90758000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr4:90756800-90758200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:90756800-90758200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:90756800-90759600	Active TSS	Ovary	ovary
25	chr4:90756800-90759800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr4:90757000-90757400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
27	chr4:90757000-90757400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr4:90757000-90757400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
29	chr4:90757000-90757400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr4:90757000-90757400	Active TSS	Colon Smooth Muscle	Colon
31	chr4:90757000-90757400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
32	chr4:90757000-90757400	Bivalent/Poised TSS	Fetal Lung	lung
33	chr4:90757000-90757400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr4:90757000-90757600	Active TSS	Brain Germinal Matrix	brain
35	chr4:90757000-90758000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr4:90757000-90758000	Bivalent/Poised TSS	Fetal Kidney	kidney
37	chr4:90757000-90758200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr4:90757000-90758200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr4:90757000-90758200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr4:90757000-90759400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:90757000-90759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:90757000-90759600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:90757200-90757400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:90757200-90757400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr4:90757200-90757400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:90757200-90757400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr4:90757200-90757400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:90757200-90757400	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr4:90757200-90757400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
50	chr4:90757200-90757400	Active TSS	Esophagus	oesophagus

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