Variant report

Variant	rs2299640
Chromosome Location	chr11:17441228-17441229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11024284	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12280242	1.00[ASN][1000 genomes]
rs12280281	1.00[ASN][1000 genomes]
rs12293228	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1805036	1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs2299638	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4148624	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4148627	1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs4148634	1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[ASN][1000 genomes]
rs4756888	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7926934	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs7932122	1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs7939973	1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs7944045	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs929235	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299640	C11orf58	cis	cerebellum	SCAN
rs2299640	HPS5	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17418600-17453600	Weak transcription	Fetal Brain Female	brain
2	chr11:17428200-17450200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:17435000-17442000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:17435000-17442200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:17435000-17443200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr11:17435200-17460600	Weak transcription	Right Atrium	heart
7	chr11:17437400-17445000	Weak transcription	Pancreas	Pancrea
8	chr11:17437600-17442600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:17437800-17448000	Enhancers	Dnd41	blood
10	chr11:17440400-17443400	Weak transcription	Fetal Thymus	thymus
11	chr11:17440800-17442200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:17441000-17442000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:17441200-17442200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr11:17441200-17442400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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Input of quick search could be:

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

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