Variant report

Variant	rs335789
Chromosome Location	chr15:60335667-60335668
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10851671	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs11071497	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441322	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1559774	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2007037	0.81[ASN][1000 genomes]
rs335788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs335791	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4775234	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62003056	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904280	chr15:60042722-60524025	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833028	chr15:60227565-60418112	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv569607	chr15:60303749-60347452	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1043235	chr15:60318001-60350625	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1044105	chr15:60318001-60354519	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1038620	chr15:60319463-60349494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv542404	chr15:60319463-60349494	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045741	chr15:60323323-60350625	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs335789	CCNB2	cis	cerebellum	SCAN
rs335789	TEX9	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:60330600-60336400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:60332200-60336400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:60334000-60344200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:60334200-60336200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:60334400-60336400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:60334600-60335800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:60334800-60336200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:60334800-60336200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:60334800-60336400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:60335000-60336200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:60335000-60336200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:60335200-60336200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:60335400-60336200	Enhancers	Dnd41	blood
14	chr15:60335600-60336600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:60335600-60337600	Enhancers	Thymus	Thymus

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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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