Variant report

Variant	rs12439646
Chromosome Location	chr15:29704000-29704001
allele	C/T
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:16)

rs_ID	r²[population]
rs11072884	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11632507	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11857622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12438851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440510	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1520936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1520937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17670431	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56392156	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56954362	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58303225	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59523689	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59588600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66493877	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67487048	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72719529	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv3364436	chr15:29459739-29853229	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh 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

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29696800-29704000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:29702600-29706000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:29702800-29704600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:29703000-29704800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:29703000-29705400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:29703000-29705600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:29704000-29704200	Enhancers	H9 Cell Line	embryonic stem cell
8	chr15:29704000-29704200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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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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