Variant report

Variant	rs1899389
Chromosome Location	chr4:90802998-90802999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10001067	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10004413	0.88[EUR][1000 genomes]
rs10005233	0.83[MEX][hapmap]
rs10028246	0.83[EUR][1000 genomes]
rs12331318	0.88[EUR][1000 genomes]
rs1348224	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1372507	0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1372517	0.83[AMR][1000 genomes]
rs1372521	0.84[EUR][1000 genomes]
rs1372522	0.84[EUR][1000 genomes]
rs1442129	0.85[CHD][hapmap]
rs1442134	0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1442135	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442140	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471483	0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs1822217	0.82[EUR][1000 genomes]
rs2011543	0.82[ASN][1000 genomes]
rs2301134	0.92[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2301135	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2736994	0.98[ASN][1000 genomes]
rs28403500	0.88[EUR][1000 genomes]
rs28415623	0.83[EUR][1000 genomes]
rs28507349	0.83[EUR][1000 genomes]
rs28734152	0.88[EUR][1000 genomes]
rs28777703	0.88[EUR][1000 genomes]
rs35424815	0.88[EUR][1000 genomes]
rs3756059	0.89[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3756063	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3806789	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58864428	0.83[EUR][1000 genomes]
rs6532192	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6532193	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6532198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6812192	0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6816736	0.84[EUR][1000 genomes]
rs6817001	0.84[EUR][1000 genomes]
rs6828271	0.82[AMR][1000 genomes]
rs6831847	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843084	0.84[EUR][1000 genomes]
rs6848181	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763443	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656954	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671549	0.88[EUR][1000 genomes]
rs7672979	0.88[EUR][1000 genomes]
rs7680557	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7680761	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7681154	0.84[EUR][1000 genomes]
rs7681440	0.83[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes]
rs7687945	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7691487	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7698219	0.88[EUR][1000 genomes]
rs894280	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs920624	0.82[AMR][1000 genomes]
rs9307077	0.89[CHD][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]

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	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	nsv997700	chr4:90791866-90920021	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1899389	DSPP	cis	cerebellum	SCAN
rs1899389	FAM190A	cis	cerebellum	SCAN
rs1899389	SNCA	cis	cerebellum	SCAN
rs1899389	MMRN1	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90800200-90809200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:90802200-90803400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:90802800-90803000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:90802800-90803200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links