Variant report

Variant	rs2299638
Chromosome Location	chr11:17443587-17443588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17437268..17438845-chr11:17442068..17444697,2	K562	blood:
2	chr11:17440734..17443682-chr11:17450301..17453039,2	K562	blood:
3	chr11:17443188..17444984-chr11:17447218..17450052,2	K562	blood:
4	chr11:17431085..17433114-chr11:17442252..17444693,2	K562	blood:
5	chr11:17438853..17441304-chr11:17442560..17445643,3	K562	blood:

Variant related genes	Relation type
ENSG00000006071	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11024284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299640	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4148622	0.85[YRI][hapmap]
rs4148624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929235	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]

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
rs2299638	HPS5	cis	cerebellum	SCAN
rs2299638	C11orf58	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr11:17435200-17460600	Weak transcription	Right Atrium	heart
4	chr11:17437400-17445000	Weak transcription	Pancreas	Pancrea
5	chr11:17437800-17448000	Enhancers	Dnd41	blood
6	chr11:17441400-17444000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr11:17441600-17444200	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr11:17442600-17443800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:17442600-17443800	Enhancers	Left Ventricle	heart
10	chr11:17442600-17444000	Enhancers	Psoas Muscle	Psoas
11	chr11:17442800-17443600	Enhancers	H9 Cell Line	embryonic stem cell
12	chr11:17442800-17443600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr11:17442800-17451200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:17443000-17448000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:17443200-17443600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr11:17443200-17443800	Enhancers	Brain Substantia Nigra	brain
17	chr11:17443200-17444200	Enhancers	Brain Anterior Caudate	brain
18	chr11:17443400-17443600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:17443400-17443600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:17443400-17443600	Enhancers	Fetal Intestine Small	intestine
21	chr11:17443400-17443600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr11:17443400-17443600	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr11:17443400-17443800	Enhancers	Fetal Thymus	thymus
24	chr11:17443400-17444200	Enhancers	Brain Angular Gyrus	brain

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