Variant report

Variant	rs2399411
Chromosome Location	chr3:112029579-112029580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11714917	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716857	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073116	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17513726	0.83[ASN][1000 genomes]
rs2280462	0.91[ASN][1000 genomes]
rs4234416	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4550804	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56037521	0.83[ASN][1000 genomes]
rs62264134	0.83[ASN][1000 genomes]
rs62264135	0.83[ASN][1000 genomes]
rs62264136	0.83[ASN][1000 genomes]
rs62264137	0.83[ASN][1000 genomes]
rs6438066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438067	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438068	0.91[ASN][1000 genomes]
rs6771014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774405	0.91[ASN][1000 genomes]
rs6809034	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7619941	0.91[ASN][1000 genomes]
rs939576	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939577	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939578	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814088	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818526	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3336356	chr3:112027218-112031669	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112025200-112034600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:112027400-112029800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:112027400-112031400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:112027400-112032800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:112027600-112030800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:112027600-112032800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:112027600-112033000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:112028600-112030000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:112028600-112034000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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