Variant report

Variant	rs41620
Chromosome Location	chr7:120425818-120425819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10266755	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10274689	0.87[CEU][hapmap]
rs114420	0.84[EUR][1000 genomes]
rs12154976	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs13231854	0.83[EUR][1000 genomes]
rs17142976	0.82[CEU][hapmap]
rs17142995	0.81[CEU][hapmap]
rs2107275	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2189974	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs3735467	0.81[EUR][1000 genomes]
rs3823861	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs41611	0.83[EUR][1000 genomes]
rs41612	0.82[EUR][1000 genomes]
rs41613	0.86[EUR][1000 genomes]
rs41616	0.87[EUR][1000 genomes]
rs41617	0.88[EUR][1000 genomes]
rs41618	0.84[EUR][1000 genomes]
rs41619	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41621	0.94[EUR][1000 genomes]
rs41622	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs41623	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs41624	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs41626	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41627	0.91[EUR][1000 genomes]
rs41628	0.94[EUR][1000 genomes]
rs41629	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs41632	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs42333	0.84[EUR][1000 genomes]
rs4730982	0.95[CEU][hapmap]
rs6953454	0.87[CEU][hapmap]
rs73425863	0.86[ASN][1000 genomes]
rs7805733	0.86[CEU][hapmap]
rs996903	0.86[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41620	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120423000-120426000	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr7:120423000-120449200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:120424600-120426000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr7:120424800-120426000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:120424800-120426000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr7:120425600-120433200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:120425600-120434400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:120425600-120434400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:120425800-120427800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:120425800-120432400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:120425800-120434800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:120425800-120437600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:120425800-120454400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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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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