Variant report

Variant	rs12488298
Chromosome Location	chr3:99246396-99246397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10935836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12488332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496937	0.98[EUR][1000 genomes]
rs1398739	0.98[EUR][1000 genomes]
rs1513297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1513313	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17775207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17775314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59039617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440679	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6765526	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6804164	0.94[ASN][1000 genomes]
rs73134321	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73134343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73144669	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7646873	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3422853	chr3:99208019-99342748	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99242600-99254000	Weak transcription	HUVEC	blood vessel
2	chr3:99243400-99248400	Weak transcription	NHDF-Ad	bronchial
3	chr3:99243400-99251000	Weak transcription	Osteobl	bone
4	chr3:99243600-99247800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:99245600-99246400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:99245600-99246800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:99245600-99247000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:99245800-99246400	Enhancers	Fetal Heart	heart
9	chr3:99245800-99247000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:99246000-99246400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:99246000-99246400	Enhancers	HSMMtube	muscle
12	chr3:99246000-99246600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:99246000-99246800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr3:99246000-99247000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:99246200-99247000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:99246200-99247000	Enhancers	Aorta	Aorta
17	chr3:99246200-99254200	Weak transcription	NHLF	lung

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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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