Variant report

Variant	rs12340534
Chromosome Location	chr9:27310415-27310416
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10217148	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10967879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967880	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967890	1.00[MEX][hapmap]
rs12001452	1.00[MEX][hapmap]
rs12335860	1.00[AMR][1000 genomes]
rs12335897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12337261	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12342167	0.87[AFR][1000 genomes]
rs12342171	0.82[AFR][1000 genomes]
rs12349825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1019688	chr9:27234184-27356374	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv466337	chr9:27250868-27353460	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv613949	chr9:27250868-27353460	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv892866	chr9:27274370-27332818	Bivalent Enhancer Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12340534	CRY1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27304400-27311800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:27305000-27312200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:27308400-27310600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
4	chr9:27308400-27310800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:27308400-27311200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:27308600-27311200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr9:27308600-27312400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:27309200-27313800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:27309400-27312000	Weak transcription	Brain Germinal Matrix	brain
10	chr9:27309400-27312400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:27309600-27310600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr9:27309600-27311000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr9:27309800-27311400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:27310200-27310600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:27310200-27310800	Weak transcription	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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