Variant report

Variant	rs12082740
Chromosome Location	chr1:160743826-160743827
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11265473	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11582702	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12064520	0.88[EUR][1000 genomes]
rs12068654	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1328111	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2176873	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs477299	0.86[EUR][1000 genomes]
rs504170	0.88[EUR][1000 genomes]
rs518242	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs528095	0.88[EUR][1000 genomes]
rs546757	0.88[EUR][1000 genomes]
rs564833	0.88[EUR][1000 genomes]
rs564883	0.97[EUR][1000 genomes]
rs574491	0.88[EUR][1000 genomes]
rs579821	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428532	chr1:160671125-160767708	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv947134	chr1:160742631-160749214	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12082740	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs12082740	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160738200-160745200	Weak transcription	Primary B cells from cord blood	blood
2	chr1:160738400-160747400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:160738600-160744800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:160740400-160744800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:160743200-160747400	Enhancers	GM12878-XiMat	blood
6	chr1:160743600-160744000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:160743800-160745200	Weak transcription	Esophagus	oesophagus

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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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