Variant report

Variant	rs10879729
Chromosome Location	chr12:74444514-74444515
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10748252	0.93[EUR][1000 genomes]
rs10879723	0.80[AMR][1000 genomes]
rs11179944	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1357241	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs1516293	0.82[AMR][1000 genomes]
rs1546728	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1546729	0.81[EUR][1000 genomes]
rs1829698	0.81[CHB][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2365429	0.82[AMR][1000 genomes]
rs2365432	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4883498	0.82[AMR][1000 genomes]
rs7136417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs7316611	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7969831	0.89[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][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	nsv1037030	chr12:73898311-74656764	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv541537	chr12:73898311-74656764	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv2755812	chr12:74110833-74557833	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv899282	chr12:74315252-74505531	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv469469	chr12:74355828-74505531	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv559391	chr12:74355828-74505531	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv899283	chr12:74360978-74609860	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10879729	TSPAN8	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74444000-74446200	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr12:74444200-74445000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:74444200-74445600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:74444200-74445800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr12:74444400-74445800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr12:74444400-74446200	Enhancers	HUES6 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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