Variant report

Variant	rs13412640
Chromosome Location	chr2:99634099-99634100
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99633286..99635570-chr2:99636929..99639924,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10165534	0.90[AMR][1000 genomes]
rs10179043	0.88[AMR][1000 genomes]
rs10196680	0.88[AMR][1000 genomes]
rs12464710	0.90[AMR][1000 genomes]
rs12467679	0.90[AMR][1000 genomes]
rs12473029	0.84[AMR][1000 genomes]
rs12477754	0.88[AMR][1000 genomes]
rs12477978	0.84[AMR][1000 genomes]
rs1349778	0.90[AMR][1000 genomes]
rs1349779	0.84[AMR][1000 genomes]
rs1580068	0.90[AMR][1000 genomes]
rs17708218	0.85[AMR][1000 genomes]
rs1993230	0.88[AMR][1000 genomes]
rs2045057	0.88[AMR][1000 genomes]
rs2309524	0.90[AMR][1000 genomes]
rs4622780	0.90[AMR][1000 genomes]
rs6542852	0.85[AMR][1000 genomes]
rs6542858	0.87[AMR][1000 genomes]
rs6704766	0.90[AMR][1000 genomes]
rs6736064	0.90[AMR][1000 genomes]
rs6759354	0.90[AMR][1000 genomes]
rs7558239	0.90[AMR][1000 genomes]
rs896886	0.90[AMR][1000 genomes]
rs9308816	0.90[AMR][1000 genomes]
rs972768	0.88[AMR][1000 genomes]
rs9808541	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv2844	chr2:99594062-99638761	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv979072	chr2:99613444-99652736	ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13412640	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs13412640	TSGA10	cis	Esophagus Mucosa	GTEx
rs13412640	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99627600-99658800	Weak transcription	Pancreas	Pancrea
2	chr2:99633400-99634600	Weak transcription	Ovary	ovary

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