Variant report

Variant	rs2952278
Chromosome Location	chr17:66479216-66479217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11656906	1.00[ASW][hapmap];0.93[YRI][hapmap]
rs12943181	0.87[ASW][hapmap]
rs2286559	1.00[CHB][hapmap]
rs2302782	1.00[ASW][hapmap];0.86[YRI][hapmap]
rs2860302	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2907373	0.86[YRI][hapmap]
rs2952282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952291	1.00[ASW][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs6501512	0.89[GIH][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap]
rs7207491	0.84[YRI][hapmap]
rs7222188	0.86[YRI][hapmap]
rs8066131	0.83[GIH][hapmap]
rs8076465	0.86[YRI][hapmap]
rs8080306	1.00[CHB][hapmap]
rs918167	1.00[ASW][hapmap];0.92[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2952278	PITPNC1	cis	cerebellum	SCAN
rs2952278	PRKAR1A	cis	multi-tissue	Pritchard
rs2952278	SAMD4B	trans	cerebellum	SCAN
rs2952278	WIPI1	cis	parietal	SCAN
rs2952278	CD79B	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66467800-66487000	Weak transcription	Right Atrium	heart
2	chr17:66477000-66480200	Enhancers	HepG2	liver
3	chr17:66477400-66483600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:66478000-66479600	Enhancers	Ovary	ovary
5	chr17:66478200-66484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:66478400-66487600	Weak transcription	Gastric	stomach
7	chr17:66478800-66479400	Enhancers	Liver	Liver
8	chr17:66478800-66479400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr17:66478800-66479600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr17:66479200-66479600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:66479200-66480200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:66479200-66480200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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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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