Variant report

Variant	rs2301135
Chromosome Location	chr4:90758389-90758390
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	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	MYC	chr4:90757889-90758516	MCF10A-Er-Src	breast:	n/a	chr4:90758080-90758090
4	CHD2	chr4:90758093-90758506	H1-hESC	embryonic stem cell:	n/a	chr4:90758387-90758397
5	MAX	chr4:90757886-90758637	SK-N-SH	brain:	n/a	chr4:90758080-90758090
6	POLR2A	chr4:90757941-90759580	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr4:90758000-90758525	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr4:90757982-90759110	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
9	FOXP2	chr4:90758001-90758434	SK-N-MC	brain:	n/a	n/a
10	TAF1	chr4:90758136-90758591	H1-neurons	neurons:	n/a	n/a
11	E2F6	chr4:90757956-90758737	K562	blood:	n/a	chr4:90758514-90758521 chr4:90758510-90758522 chr4:90758514-90758521 chr4:90758464-90758473 chr4:90758511-90758525 chr4:90758514-90758521
12	YY1	chr4:90758069-90758557	H1-hESC	embryonic stem cell:	n/a	chr4:90758461-90758475 chr4:90758401-90758415 chr4:90758458-90758469
13	MAX	chr4:90757837-90758599	ECC-1	luminal epithelium:	n/a	chr4:90758080-90758090
14	POLR2A	chr4:90758021-90758573	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr4:90758121-90758402	H1-hESC	embryonic stem cell:	n/a	n/a
16	E2F6	chr4:90757916-90758485	A549	lung:	n/a	chr4:90758464-90758473
17	POLR2A	chr4:90758068-90759085	HEK293	kidney:	n/a	n/a
18	POLR2A	chr4:90758377-90758573	K562	blood:	n/a	n/a
19	GATA2	chr4:90757246-90759504	SH-SY5Y	brain:	n/a	chr4:90758439-90758447 chr4:90758097-90758105
20	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
21	MAX	chr4:90757952-90758985	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
22	ZBTB7A	chr4:90757811-90758759	ECC-1	luminal epithelium:	n/a	chr4:90758721-90758732 chr4:90758722-90758733 chr4:90758277-90758286 chr4:90758463-90758472 chr4:90758523-90758532
23	MAX	chr4:90757960-90758701	SK-N-SH	brain:	n/a	chr4:90758080-90758090
24	POLR2A	chr4:90757959-90759244	HUVEC	blood vessel:	n/a	n/a
25	TBP	chr4:90757998-90759047	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr4:90757883-90759635	H1-neurons	neurons:	n/a	n/a
27	BACH1	chr4:90757699-90758463	H1-hESC	embryonic stem cell:	n/a	n/a
28	SP4	chr4:90758220-90758688	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr4:90757892-90759167	HUVEC	blood vessel:	n/a	n/a
30	E2F6	chr4:90758379-90758621	K562	blood:	n/a	chr4:90758514-90758521 chr4:90758510-90758522 chr4:90758514-90758521 chr4:90758464-90758473 chr4:90758511-90758525 chr4:90758514-90758521
31	POLR2A	chr4:90758092-90758831	SK-N-MC	brain:	n/a	n/a
32	MAX	chr4:90757945-90758422	A549	lung:	n/a	chr4:90758080-90758090
33	ZBTB7A	chr4:90757973-90758730	ECC-1	luminal epithelium:	n/a	chr4:90758277-90758286 chr4:90758463-90758472 chr4:90758523-90758532
34	JUND	chr4:90758106-90758884	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr4:90757970-90759061	PBDE	blood:	n/a	n/a
36	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
37	SIN3A	chr4:90757284-90759458	H1-hESC	embryonic stem cell:	n/a	chr4:90759043-90759052
38	MAX	chr4:90757782-90758982	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
39	MAX	chr4:90757869-90758613	HCT-116	colon:	n/a	chr4:90758080-90758090
40	POLR2A	chr4:90757951-90758499	HUVEC	blood vessel:	n/a	n/a
41	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
42	ZNF263	chr4:90757349-90758919	K562	blood:	n/a	chr4:90757923-90757932
43	CTBP2	chr4:90757235-90758898	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr4:90757794-90758579	ECC-1	luminal epithelium:	n/a	chr4:90758080-90758090
45	MAX	chr4:90757979-90758532	K562	blood:	n/a	chr4:90758080-90758090
46	POLR2A	chr4:90757921-90759119	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAZ	chr4:90757933-90758583	IMR90	lung:	n/a	chr4:90758080-90758090
48	MAX	chr4:90757924-90758565	HCT-116	colon:	n/a	chr4:90758080-90758090
49	POLR2A	chr4:90757983-90759083	MCF10A-Er-Src	breast:	n/a	n/a
50	SIN3AK20	chr4:90758056-90758572	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SNCA	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10004413	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10005233	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10008964	0.91[ASN][1000 genomes]
rs10028246	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12331318	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1348224	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372517	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1372518	0.91[ASN][1000 genomes]
rs1372519	0.91[ASN][1000 genomes]
rs1372520	0.91[ASN][1000 genomes]
rs1372521	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1372522	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1442135	0.82[EUR][1000 genomes]
rs1442140	0.82[EUR][1000 genomes]
rs1442144	0.91[ASN][1000 genomes]
rs1442148	0.94[ASN][1000 genomes]
rs1471483	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1471484	0.91[ASN][1000 genomes]
rs1811442	0.94[ASN][1000 genomes]
rs1811443	0.94[ASN][1000 genomes]
rs1822217	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1837891	0.91[ASN][1000 genomes]
rs184810	0.89[ASN][1000 genomes]
rs1899389	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2197120	0.91[ASN][1000 genomes]
rs2245801	1.00[ASN][1000 genomes]
rs2301134	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572318	0.91[ASN][1000 genomes]
rs2572320	0.91[ASN][1000 genomes]
rs2583962	0.91[ASN][1000 genomes]
rs2583964	0.91[ASN][1000 genomes]
rs2583968	0.93[ASN][1000 genomes]
rs2583972	0.94[ASN][1000 genomes]
rs2583975	0.94[ASN][1000 genomes]
rs2583978	0.90[ASN][1000 genomes]
rs2619341	0.91[ASN][1000 genomes]
rs2619347	0.93[ASN][1000 genomes]
rs2619349	0.94[ASN][1000 genomes]
rs2619355	0.94[ASN][1000 genomes]
rs2619356	0.90[ASN][1000 genomes]
rs2619368	0.91[ASN][1000 genomes]
rs2737002	0.91[ASN][1000 genomes]
rs2737010	0.90[ASN][1000 genomes]
rs2737011	0.94[ASN][1000 genomes]
rs2737021	0.91[ASN][1000 genomes]
rs2737025	0.91[ASN][1000 genomes]
rs2737028	0.91[ASN][1000 genomes]
rs2737030	0.91[ASN][1000 genomes]
rs28403500	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28415623	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28507349	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28734152	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28777703	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3113355	0.93[ASN][1000 genomes]
rs35424815	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356162	0.89[ASN][1000 genomes]
rs356186	0.91[ASN][1000 genomes]
rs356188	0.85[ASN][1000 genomes]
rs356191	0.88[ASN][1000 genomes]
rs3756059	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756063	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3806789	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4293762	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58864428	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532191	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532192	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532193	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6816736	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6817001	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6828271	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6831847	0.83[EUR][1000 genomes]
rs6839608	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6843084	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6848181	0.83[EUR][1000 genomes]
rs748849	0.91[ASN][1000 genomes]
rs763443	0.81[EUR][1000 genomes]
rs7656954	0.83[EUR][1000 genomes]
rs7671549	0.91[EUR][1000 genomes]
rs7672979	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7680557	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680761	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7681154	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7681440	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7687945	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7698219	0.91[EUR][1000 genomes]
rs894280	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs920624	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs990085	0.91[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
rs2301135	SNCA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr4:90756600-90758600	Enhancers	Spleen	Spleen
5	chr4:90756600-90759000	Active TSS	Brain Substantia Nigra	brain
6	chr4:90756600-90759400	Active TSS	Brain Anterior Caudate	brain
7	chr4:90756600-90759600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr4:90756800-90759600	Active TSS	Ovary	ovary
9	chr4:90756800-90759800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr4:90757000-90759400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:90757000-90759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:90757000-90759600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:90757200-90758800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
14	chr4:90757200-90758800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
15	chr4:90757200-90759400	Active TSS	Brain Hippocampus Middle	brain
16	chr4:90757200-90759600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:90757200-90759600	Active TSS	Brain Cingulate Gyrus	brain
18	chr4:90757200-90759800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:90757400-90758400	Flanking Active TSS	Pancreas	Pancrea
20	chr4:90757400-90758600	Bivalent/Poised TSS	Psoas Muscle	Psoas
21	chr4:90757400-90758800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
22	chr4:90757400-90758800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
23	chr4:90757400-90758800	Bivalent/Poised TSS	NHDF-Ad	bronchial
24	chr4:90757400-90759000	Active TSS	HMEC	breast
25	chr4:90757400-90759400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
26	chr4:90757400-90759400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
27	chr4:90757400-90759400	Active TSS	Right Atrium	heart
28	chr4:90757400-90759600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr4:90757400-90759600	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr4:90757400-90759600	Active TSS	Brain Angular Gyrus	brain
31	chr4:90757400-90759600	Active TSS	Fetal Brain Male	brain
32	chr4:90757400-90760200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:90757600-90758400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
34	chr4:90757600-90758600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:90757600-90758600	Active TSS	Liver	Liver
36	chr4:90757600-90758600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
37	chr4:90757600-90758800	Active TSS	Hela-S3	cervix
38	chr4:90757600-90759000	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr4:90757600-90759000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
40	chr4:90757600-90759000	Active TSS	HUVEC	blood vessel
41	chr4:90757600-90759200	Bivalent/Poised TSS	Left Ventricle	heart
42	chr4:90757600-90759400	Bivalent/Poised TSS	Esophagus	oesophagus
43	chr4:90757600-90759400	Active TSS	K562	blood
44	chr4:90757600-90759600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:90757800-90758400	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:90757800-90758400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:90757800-90758600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
48	chr4:90757800-90758600	Weak transcription	Fetal Heart	heart
49	chr4:90757800-90758600	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr4:90757800-90758600	Bivalent/Poised TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links