Variant report

Variant	rs4698412
Chromosome Location	chr4:15737348-15737349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15655679..15657937-chr4:15737188..15739918,2	K562	blood:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10516290	0.82[JPT][hapmap]
rs10516291	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1058212	0.82[JPT][hapmap]
rs11724635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931532	0.82[JPT][hapmap]
rs11944132	0.82[JPT][hapmap]
rs12645513	0.84[JPT][hapmap]
rs12645693	0.82[JPT][hapmap]
rs12646331	0.82[JPT][hapmap]
rs12651052	0.82[JPT][hapmap]
rs16892271	0.82[JPT][hapmap]
rs16892272	0.82[JPT][hapmap]
rs16892276	0.82[JPT][hapmap]
rs16892283	0.82[JPT][hapmap]
rs16892287	0.82[JPT][hapmap]
rs16892289	0.82[JPT][hapmap]
rs16898413	0.82[JPT][hapmap]
rs2286879	0.81[CHB][hapmap]
rs3213710	0.82[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs34559912	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4263397	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[ASN][1000 genomes]
rs4266290	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4273468	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4321629	0.82[JPT][hapmap]
rs4389574	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4403048	0.99[ASN][1000 genomes]
rs4435745	0.82[JPT][hapmap]
rs4498133	0.82[JPT][hapmap]
rs4538475	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4541502	0.85[GIH][hapmap]
rs4613561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4698119	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4698120	0.81[CHB][hapmap]
rs4698413	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449168	0.97[ASN][1000 genomes]
rs6835705	0.82[JPT][hapmap]
rs6844968	0.82[JPT][hapmap]
rs955410	0.82[JPT][hapmap]
rs9790670	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Parkinson's disease	21084426	GWAS catalog
Parkinson's disease	22451204	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4698412	FGFBP2	cis	parietal	SCAN
rs4698412	CASP9	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15707400-15742800	Weak transcription	Primary B cells from cord blood	blood
2	chr4:15708800-15739400	Weak transcription	Ovary	ovary
3	chr4:15723000-15743000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:15723000-15744600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:15726000-15737400	Weak transcription	NHLF	lung
6	chr4:15726000-15740200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:15727400-15740400	Weak transcription	Fetal Intestine Large	intestine
8	chr4:15729000-15743200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:15732000-15738800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:15733600-15742800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:15735400-15739000	Weak transcription	Fetal Intestine Small	intestine
12	chr4:15735400-15742800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:15735800-15737400	Enhancers	Fetal Thymus	thymus
14	chr4:15735800-15740200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr4:15736400-15739000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:15736400-15739200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:15736600-15739000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:15736800-15737800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:15737200-15738400	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links