Variant report

Variant	rs2619361
Chromosome Location	chr4:90757735-90757736
allele	A/C
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	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	GATA2	chr4:90757246-90759504	SH-SY5Y	brain:	n/a	chr4:90758439-90758447 chr4:90758097-90758105
3	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr4:90757700-90757850	AG09319	gingival:	n/a	n/a
5	BACH1	chr4:90757699-90758463	H1-hESC	embryonic stem cell:	n/a	n/a
6	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
7	SIN3A	chr4:90757284-90759458	H1-hESC	embryonic stem cell:	n/a	chr4:90759043-90759052
8	POLR2A	chr4:90756656-90757751	PBDE	blood:	n/a	n/a
9	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
10	ZNF263	chr4:90757349-90758919	K562	blood:	n/a	chr4:90757923-90757932
11	CTBP2	chr4:90757235-90758898	H1-hESC	embryonic stem cell:	n/a	n/a
12	GATA1	chr4:90756797-90758328	PBDE	blood:	n/a	chr4:90758097-90758105
13	ZNF263	chr4:90757362-90759526	HEK293-T-REx	kidney:	n/a	chr4:90757923-90757932

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MMRN1-1	chr4:90757559-90757885	ENSG00000247775
2	lnc-MMRN1-1	chr4:90757575-90757885	ENSG00000247775
3	lnc-MMRN1-1	chr4:90757552-90757885	NONHSAT097403

Variant related genes	Relation type
SNCA	TF binding region

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

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

rs_ID	r²[population]
rs13142587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1372516	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1442146	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1442147	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1442149	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2028535	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2165614	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2583958	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2583959	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2583965	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2583966	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2583967	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583969	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583970	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583971	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583973	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583974	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583976	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2583977	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583980	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583981	1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583983	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583984	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583985	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2619344	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2619345	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2619346	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2619348	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619350	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619353	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619354	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619358	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619359	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619360	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619362	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619363	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	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2619371	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2619373	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2736995	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2736996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2736997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2736998	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2736999	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737000	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737004	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737006	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737008	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737009	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737012	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737013	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737014	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2737015	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2737016	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2737017	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2737018	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2737019	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737022	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2737023	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2737024	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2737033	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2737035	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs33965306	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs356163	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356184	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356185	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356187	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356189	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356192	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356195	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs356199	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67876224	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs986609	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs986610	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs990086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs990087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs990088	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:114 , 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	chr4:90756200-90757800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:90756600-90758000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:90756600-90758000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:90756600-90758600	Enhancers	Spleen	Spleen
8	chr4:90756600-90759000	Active TSS	Brain Substantia Nigra	brain
9	chr4:90756600-90759400	Active TSS	Brain Anterior Caudate	brain
10	chr4:90756600-90759600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr4:90756800-90758000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:90756800-90758000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr4:90756800-90758200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr4:90756800-90758200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:90756800-90759600	Active TSS	Ovary	ovary
16	chr4:90756800-90759800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr4:90757000-90758000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr4:90757000-90758000	Bivalent/Poised TSS	Fetal Kidney	kidney
19	chr4:90757000-90758200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr4:90757000-90758200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr4:90757000-90758200	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr4:90757000-90759400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:90757000-90759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:90757000-90759600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:90757200-90757800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr4:90757200-90757800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:90757200-90757800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr4:90757200-90758000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr4:90757200-90758000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr4:90757200-90758000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
31	chr4:90757200-90758200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:90757200-90758200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr4:90757200-90758200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr4:90757200-90758800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
35	chr4:90757200-90758800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
36	chr4:90757200-90759400	Active TSS	Brain Hippocampus Middle	brain
37	chr4:90757200-90759600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:90757200-90759600	Active TSS	Brain Cingulate Gyrus	brain
39	chr4:90757200-90759800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:90757400-90757800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:90757400-90757800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:90757400-90757800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr4:90757400-90757800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
44	chr4:90757400-90757800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:90757400-90757800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
46	chr4:90757400-90757800	Enhancers	Fetal Heart	heart
47	chr4:90757400-90757800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
48	chr4:90757400-90757800	Flanking Active TSS	Lung	lung
49	chr4:90757400-90757800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr4:90757400-90757800	Flanking Bivalent TSS/Enh	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links