Variant report

Variant	rs1792313
Chromosome Location	chr11:71075608-71075609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1660873	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1660874	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1660879	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1660884	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1660891	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790318	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790321	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790338	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792215	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792252	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792333	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs999124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1792313	SHANK2	cis	lymphoblastoid	seeQTL
rs1792313	C11orf24	cis	cerebellum	SCAN
rs1792313	ING1	trans	parietal	SCAN
rs1792313	RNF169	cis	parietal	SCAN
rs1792313	ACY3	cis	cerebellum	SCAN
rs1792313	C2CD3	cis	cerebellum	SCAN
rs1792313	KRTAP5-9	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71074400-71076400	Enhancers	Brain Cingulate Gyrus	brain
2	chr11:71074400-71076400	Enhancers	Brain Substantia Nigra	brain
3	chr11:71074400-71076600	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr11:71074600-71076200	Enhancers	Fetal Muscle Leg	muscle
5	chr11:71074600-71076400	Enhancers	Brain Angular Gyrus	brain
6	chr11:71074800-71076000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:71074800-71076000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr11:71074800-71076000	Enhancers	HSMM	muscle
9	chr11:71074800-71076000	Enhancers	HSMMtube	muscle
10	chr11:71074800-71076200	Enhancers	Brain Anterior Caudate	brain
11	chr11:71074800-71076200	Enhancers	Fetal Muscle Trunk	muscle
12	chr11:71074800-71076400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:71075200-71075800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:71075400-71075800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:71075400-71075800	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr11:71075400-71075800	Enhancers	Pancreas	Pancrea

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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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