Variant report

Variant	rs9864302
Chromosome Location	chr3:140477828-140477829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12486650	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1561764	0.80[ASN][1000 genomes]
rs35776063	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4571221	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57525460	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6793208	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7618025	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7630239	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7645792	0.97[EUR][1000 genomes]
rs9836729	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1008838	chr3:140355975-140588726	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877547	chr3:140366948-140575287	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv829743	chr3:140384246-140559778	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9864302	CLSTN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140473800-140479200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:140474000-140478000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:140474000-140478200	Weak transcription	Thymus	Thymus
4	chr3:140474000-140479200	Weak transcription	Pancreas	Pancrea
5	chr3:140475400-140478000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:140475600-140478400	Enhancers	GM12878-XiMat	blood
7	chr3:140476600-140478000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:140477600-140478000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:140477600-140479000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:140477800-140478200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr3:140477800-140478400	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr3:140477800-140479400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:140477800-140480200	Enhancers	Fetal Thymus	thymus
14	chr3:140477800-140480400	Enhancers	Fetal Muscle Leg	muscle

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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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