Variant report

Variant	rs10435919
Chromosome Location	chr9:95296135-95296136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10115937	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10120210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10120292	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992439	0.83[CEU][hapmap]
rs1111047	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1536423	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap]
rs2007245	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2131918	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296668	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744142	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6479424	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479427	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7043114	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7864757	0.82[EUR][1000 genomes]
rs7873646	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs912260	0.92[CEU][hapmap]
rs9886781	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9969804	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.81[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	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10435919	ZNF484	cis	parietal	SCAN
rs10435919	IPPK	cis	cerebellum	SCAN
rs10435919	CENPP	cis	parietal	SCAN
rs10435919	CENPP	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95269800-95298800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:95276000-95296600	Weak transcription	Colon Smooth Muscle	Colon
3	chr9:95280800-95296400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:95284000-95296400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:95287000-95296600	Weak transcription	Ovary	ovary
6	chr9:95293200-95296400	Weak transcription	Adipose Nuclei	Adipose
7	chr9:95294000-95297000	Weak transcription	Left Ventricle	heart
8	chr9:95294200-95296400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:95294800-95296600	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:95294800-95296600	Weak transcription	Fetal Lung	lung
11	chr9:95294800-95301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:95295200-95297000	Weak transcription	Psoas Muscle	Psoas
13	chr9:95295800-95296400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:95295800-95296400	Enhancers	GM12878-XiMat	blood
15	chr9:95295800-95296800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr9:95295800-95296800	Enhancers	Liver	Liver
17	chr9:95296000-95296400	Weak transcription	Aorta	Aorta
18	chr9:95296000-95301800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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