Variant report

Variant	rs10477928
Chromosome Location	chr5:108018082-108018083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10039131	0.80[ASN][1000 genomes]
rs10477427	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11952230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11952282	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35842524	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4957781	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56915053	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703883	1.00[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];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7704020	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7704155	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7704581	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7735104	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7737443	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1024076	chr5:107991426-108028223	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1034158	chr5:107995509-108018395	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10477928	STARD4	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108007000-108034800	Weak transcription	Right Atrium	heart
2	chr5:108014200-108020800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:108017400-108021000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:108017400-108021000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:108017400-108021200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:108017400-108022000	Weak transcription	Brain Angular Gyrus	brain
7	chr5:108017600-108018200	Enhancers	GM12878-XiMat	blood
8	chr5:108017600-108018400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:108017600-108020800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:108017600-108021000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:108017600-108021200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:108017600-108021200	Weak transcription	HepG2	liver
13	chr5:108017600-108021600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:108017600-108023600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:108017600-108023600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr5:108017800-108020800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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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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