Variant report

Variant	rs2619364
Chromosome Location	chr4:90759887-90759888
allele	A/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	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
2	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
3	GATA1	chr4:90758615-90760183	PBDE	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MMRN1-1	chr4:90759412-90761746	ENSG00000247775

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	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1372516	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1442146	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1442147	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1442149	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2028535	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2165614	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2583958	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2583959	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2583965	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2583966	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2583967	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2583969	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583970	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583971	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583973	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583974	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583976	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583977	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583980	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583981	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583982	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583983	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583984	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583985	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583987	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2583988	0.83[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2583989	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2619343	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2619344	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2619345	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2619346	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2619348	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2619350	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619351	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619352	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619353	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619354	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619358	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619359	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619360	0.89[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619361	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619362	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619363	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619366	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2619367	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2619370	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2619371	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2619373	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2736995	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2736996	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736997	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736998	0.85[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736999	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737000	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737001	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737003	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737004	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737005	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737006	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737008	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737009	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737012	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737013	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737014	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737015	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737016	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737017	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737018	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2737019	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2737022	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2737023	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2737024	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2737033	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2737035	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs33965306	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs356163	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356184	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs356185	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs356187	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356189	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356192	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356195	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs356199	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67876224	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs986609	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs986610	0.89[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs990086	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs990087	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs990088	0.95[CEU][hapmap];0.98[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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90757400-90760200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:90758800-90760000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:90759000-90760000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:90759000-90760000	Flanking Active TSS	Dnd41	blood
5	chr4:90759600-90760000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:90759600-90760000	Enhancers	Primary T cells from cord blood	blood
7	chr4:90759600-90760000	Enhancers	Primary hematopoietic stem cells	blood
8	chr4:90759600-90760000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:90759600-90771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:90759800-90760000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr4:90759800-90760000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr4:90759800-90760000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr4:90759800-90760000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:90759800-90760200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr4:90759800-90760200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr4:90759800-90760200	Enhancers	HMEC	breast
17	chr4:90759800-90760400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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