Variant report

Variant	rs924447
Chromosome Location	chr5:79665173-79665174
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10037935	0.90[JPT][hapmap]
rs12055120	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12651951	0.82[JPT][hapmap]
rs12654489	0.81[JPT][hapmap]
rs13179066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16877749	1.00[ASN][1000 genomes]
rs4133093	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6876442	0.82[JPT][hapmap]
rs7703252	0.90[JPT][hapmap]
rs879738	0.80[JPT][hapmap]
rs9293816	0.85[JPT][hapmap]

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	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	49 gene(s)	inside rSNPs	diseases
2	nsv518480	chr5:79586085-79748382	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv328596	chr5:79662132-79670063	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs924447	WDR41	cis	cerebellum	SCAN
rs924447	ZFYVE16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79662200-79665200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:79663400-79667000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:79664400-79665400	Enhancers	Brain Substantia Nigra	brain
4	chr5:79664600-79665200	Enhancers	Brain Germinal Matrix	brain
5	chr5:79664600-79665400	Enhancers	Brain Anterior Caudate	brain
6	chr5:79664600-79665600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:79664800-79665200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr5:79664800-79665800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr5:79664800-79666000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:79664800-79666400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr5:79664800-79666800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:79664800-79667000	Enhancers	Brain Angular Gyrus	brain
13	chr5:79665000-79665200	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr5:79665000-79665200	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr5:79665000-79665200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr5:79665000-79665800	Enhancers	Fetal Brain Female	brain
17	chr5:79665000-79666600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:79665000-79667000	Enhancers	H1 Derived Neuronal Progenitor 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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