Variant report

Variant	rs929235
Chromosome Location	chr11:17442460-17442461
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11024284	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12280242	0.81[ASN][1000 genomes]
rs12280281	0.81[ASN][1000 genomes]
rs12293228	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1805036	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2299638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2299640	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]
rs4148622	0.81[LWK][hapmap];0.85[YRI][hapmap]
rs4148624	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4148627	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4148634	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4756888	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7926934	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7932122	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7939973	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7944045	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
rs929235	C11orf58	cis	cerebellum	SCAN
rs929235	HPS5	cis	cerebellum	SCAN

Chromatin state (count:18 , 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	chr11:17435000-17443200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr11:17435200-17460600	Weak transcription	Right Atrium	heart
5	chr11:17437400-17445000	Weak transcription	Pancreas	Pancrea
6	chr11:17437600-17442600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:17437800-17448000	Enhancers	Dnd41	blood
8	chr11:17440400-17443400	Weak transcription	Fetal Thymus	thymus
9	chr11:17441400-17444000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr11:17441600-17444200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr11:17442000-17442800	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr11:17442000-17443000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:17442000-17443200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr11:17442200-17442800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:17442200-17443400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr11:17442400-17442600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:17442400-17442800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:17442400-17443000	Enhancers	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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