Variant report

Variant	rs2301134
Chromosome Location	chr4:90758945-90758946
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	POLR2A	chr4:90758048-90759014	H1-hESC	embryonic stem cell:	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	CTCF	chr4:90758800-90758950	AG09319	gingival:	n/a	chr4:90758856-90758872
4	CTCF	chr4:90758900-90759050	GM12864	blood:	n/a	n/a
5	CTCF	chr4:90758820-90758970	GM12875	blood:	n/a	chr4:90758856-90758872
6	POLR2A	chr4:90757941-90759580	H1-neurons	neurons:	n/a	n/a
7	MAX	chr4:90757982-90759110	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
8	CTCF	chr4:90758800-90758950	RPTEC	kidney:	n/a	chr4:90758856-90758872
9	RAD21	chr4:90758632-90758976	H1-hESC	embryonic stem cell:	n/a	chr4:90758776-90758790
10	POLR2A	chr4:90758068-90759085	HEK293	kidney:	n/a	n/a
11	GATA2	chr4:90757246-90759504	SH-SY5Y	brain:	n/a	chr4:90758439-90758447 chr4:90758097-90758105
12	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
13	MAX	chr4:90757952-90758985	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
14	CTCF	chr4:90758880-90759030	RPTEC	kidney:	n/a	n/a
15	CTCF	chr4:90758840-90758990	HUVEC	blood vessel:	n/a	chr4:90758856-90758872
16	POLR2A	chr4:90757959-90759244	HUVEC	blood vessel:	n/a	n/a
17	CTCF	chr4:90758715-90759000	NHEK	skin:	n/a	chr4:90758856-90758872 chr4:90758779-90758792
18	TBP	chr4:90757998-90759047	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr4:90757883-90759635	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr4:90757892-90759167	HUVEC	blood vessel:	n/a	n/a
21	MYC	chr4:90758475-90759059	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr4:90758840-90758990	AG10803	skin:	n/a	chr4:90758856-90758872
23	MYC	chr4:90758749-90759199	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr4:90758927-90759056	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr4:90757970-90759061	PBDE	blood:	n/a	n/a
26	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
27	SIN3A	chr4:90757284-90759458	H1-hESC	embryonic stem cell:	n/a	chr4:90759043-90759052
28	MAX	chr4:90757782-90758982	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
29	RAD21	chr4:90758566-90759098	H1-hESC	embryonic stem cell:	n/a	chr4:90758776-90758790
30	KAP1	chr4:90758735-90759542	HEK293	kidney:	n/a	n/a
31	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
32	CTCF	chr4:90758779-90758989	GM12878	blood:	n/a	chr4:90758856-90758872 chr4:90758779-90758792
33	CTCF	chr4:90758840-90758990	SAEC	small airway:	n/a	chr4:90758856-90758872
34	GATA1	chr4:90758615-90760183	PBDE	blood:	n/a	n/a
35	CTCF	chr4:90758820-90758970	AG04450	lung:	n/a	chr4:90758856-90758872
36	CTCF	chr4:90758840-90758990	HEK293	kidney:	n/a	chr4:90758856-90758872
37	CTCF	chr4:90758918-90758949	Lung_OC	lung:	n/a	n/a
38	CTCF	chr4:90758900-90759050	HEEpiC	esophagus:	n/a	n/a
39	POLR2A	chr4:90757921-90759119	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr4:90758840-90758990	HFF-Myc	foreskin:	n/a	chr4:90758856-90758872
41	CTCF	chr4:90758860-90759010	BJ	skin:	n/a	n/a
42	CTCF	chr4:90758774-90758978	HUVEC	blood vessel:	n/a	chr4:90758856-90758872 chr4:90758779-90758792
43	KAP1	chr4:90758738-90759409	U2OS	brain:	n/a	n/a
44	CTCF	chr4:90758800-90758950	AG10803	skin:	n/a	chr4:90758856-90758872
45	CTCF	chr4:90758755-90758998	Medullo	brain:	n/a	chr4:90758856-90758872 chr4:90758779-90758792
46	CTCF	chr4:90758820-90758970	HBMEC	blood vessel:	n/a	chr4:90758856-90758872
47	POLR2A	chr4:90757983-90759083	MCF10A-Er-Src	breast:	n/a	n/a
48	TAF1	chr4:90758001-90759015	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr4:90758820-90758970	HCPEpiC	choroid plexus:	n/a	chr4:90758856-90758872
50	CTCF	chr4:90758880-90759030	HRPEpiC	eye:	n/a	n/a

Variant related genes	Relation type
SNCA	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10004413	0.91[EUR][1000 genomes]
rs10005233	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10008964	0.90[ASN][1000 genomes]
rs10028246	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12331318	0.91[EUR][1000 genomes]
rs1348224	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1372517	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1372518	0.90[ASN][1000 genomes]
rs1372519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1372520	0.90[ASN][1000 genomes]
rs1372521	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1372522	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1442134	0.81[CEU][hapmap]
rs1442135	0.88[CEU][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1442140	0.84[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1442144	0.90[ASN][1000 genomes]
rs1442148	0.93[ASN][1000 genomes]
rs1471483	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1471484	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1811442	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1811443	0.93[ASN][1000 genomes]
rs1822217	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1837891	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs184810	0.87[ASN][1000 genomes]
rs1899389	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2197120	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2245801	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2301135	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572318	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2572320	0.90[ASN][1000 genomes]
rs2583962	0.90[ASN][1000 genomes]
rs2583964	0.90[ASN][1000 genomes]
rs2583968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2583972	0.93[ASN][1000 genomes]
rs2583975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2583978	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2619341	0.90[ASN][1000 genomes]
rs2619347	0.91[ASN][1000 genomes]
rs2619349	0.93[ASN][1000 genomes]
rs2619355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2619356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2619368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2737002	0.90[ASN][1000 genomes]
rs2737010	0.89[ASN][1000 genomes]
rs2737011	0.93[ASN][1000 genomes]
rs2737021	0.90[ASN][1000 genomes]
rs2737025	0.90[ASN][1000 genomes]
rs2737028	0.90[ASN][1000 genomes]
rs2737030	0.90[ASN][1000 genomes]
rs28403500	0.91[EUR][1000 genomes]
rs28415623	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28507349	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28734152	0.91[EUR][1000 genomes]
rs28777703	0.91[EUR][1000 genomes]
rs3113355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35424815	0.91[EUR][1000 genomes]
rs356162	0.87[ASN][1000 genomes]
rs356186	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs356188	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs356191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3756059	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756063	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806789	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4293762	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58864428	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532191	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532192	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532193	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532198	0.92[CEU][hapmap]
rs6812192	0.81[CEU][hapmap]
rs6816736	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6817001	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6828271	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6831847	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6839608	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6843084	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6848181	0.83[EUR][1000 genomes]
rs748849	0.90[ASN][1000 genomes]
rs763443	0.88[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7656954	0.84[EUR][1000 genomes]
rs7671549	0.91[EUR][1000 genomes]
rs7672979	0.91[EUR][1000 genomes]
rs7680557	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7680761	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7681154	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7681440	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7687945	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7698219	0.91[EUR][1000 genomes]
rs894280	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs920624	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs990085	0.90[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2301134	DSPP	cis	cerebellum	SCAN
rs2301134	SNCA	Cis_1M	lymphoblastoid	RTeQTL
rs2301134	SNCA	cis	cerebellum	SCAN
rs2301134	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:122 , 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	chr4:90756600-90759000	Active TSS	Brain Substantia Nigra	brain
5	chr4:90756600-90759400	Active TSS	Brain Anterior Caudate	brain
6	chr4:90756600-90759600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr4:90756800-90759600	Active TSS	Ovary	ovary
8	chr4:90756800-90759800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr4:90757000-90759400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:90757000-90759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:90757000-90759600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:90757200-90759400	Active TSS	Brain Hippocampus Middle	brain
13	chr4:90757200-90759600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:90757200-90759600	Active TSS	Brain Cingulate Gyrus	brain
15	chr4:90757200-90759800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:90757400-90759000	Active TSS	HMEC	breast
17	chr4:90757400-90759400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
18	chr4:90757400-90759400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
19	chr4:90757400-90759400	Active TSS	Right Atrium	heart
20	chr4:90757400-90759600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr4:90757400-90759600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr4:90757400-90759600	Active TSS	Brain Angular Gyrus	brain
23	chr4:90757400-90759600	Active TSS	Fetal Brain Male	brain
24	chr4:90757400-90760200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:90757600-90759000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr4:90757600-90759000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
27	chr4:90757600-90759000	Active TSS	HUVEC	blood vessel
28	chr4:90757600-90759200	Bivalent/Poised TSS	Left Ventricle	heart
29	chr4:90757600-90759400	Bivalent/Poised TSS	Esophagus	oesophagus
30	chr4:90757600-90759400	Active TSS	K562	blood
31	chr4:90757600-90759600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:90757800-90759000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
33	chr4:90757800-90759200	Active TSS	Fetal Lung	lung
34	chr4:90757800-90759400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:90757800-90759400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:90757800-90759400	Active TSS	Lung	lung
37	chr4:90757800-90759600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr4:90757800-90759600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:90757800-90759600	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr4:90757800-90759600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:90757800-90759800	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr4:90758000-90759000	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr4:90758000-90759000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:90758000-90759000	Bivalent/Poised TSS	Thymus	Thymus
45	chr4:90758000-90759000	Active TSS	Dnd41	blood
46	chr4:90758000-90759000	Bivalent/Poised TSS	Osteobl	bone
47	chr4:90758000-90759200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr4:90758000-90759200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
49	chr4:90758000-90759600	Active TSS	H1 Cell Line	embryonic stem cell
50	chr4:90758000-90759600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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