Variant report

Variant	rs2540701
Chromosome Location	chr16:52298182-52298183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11649692	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12149208	0.81[EUR][1000 genomes]
rs12932031	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1345311	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1362377	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35641724	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71388266	0.92[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	nsv492248	chr16:51681902-52456082	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv34024	chr16:51878565-52316530	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1066719	chr16:52294981-53141905	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2540701	SLC8A1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:52280400-52301000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:52286800-52298400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr16:52286800-52299200	Weak transcription	Fetal Brain Male	brain
4	chr16:52291800-52299200	Weak transcription	Fetal Kidney	kidney
5	chr16:52296400-52299200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:52297600-52298200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr16:52297600-52302000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr16:52297600-52302000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr16:52297800-52298800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr16:52297800-52299200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr16:52297800-52299200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr16:52297800-52302200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr16:52297800-52302200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr16:52298000-52298800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr16:52298000-52299000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr16:52298000-52299200	Weak transcription	Brain Germinal Matrix	brain
17	chr16:52298000-52301800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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