Variant report

Variant	rs518721
Chromosome Location	chr1:160723517-160723518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11265473	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs12064520	0.81[EUR][1000 genomes]
rs17313034	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs17313062	0.81[EUR][1000 genomes]
rs2295616	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs3766370	0.84[CEU][hapmap];0.84[CHB][hapmap];0.87[TSI][hapmap]
rs3766373	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs3766374	0.81[EUR][1000 genomes]
rs489286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495706	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504170	0.81[EUR][1000 genomes]
rs528095	0.81[EUR][1000 genomes]
rs546757	0.81[EUR][1000 genomes]
rs549103	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs564833	0.81[EUR][1000 genomes]
rs569932	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs573702	0.84[CHB][hapmap]
rs574491	0.81[EUR][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs518721	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs518721	SLAMF7	cis	lymphoblastoid	seeQTL
rs518721	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs518721	SLAMF7	cis	multi-tissue	Pritchard
rs518721	SLAMF7	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160714400-160726800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:160717000-160724400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:160718000-160723800	Genic enhancers	GM12878-XiMat	blood
4	chr1:160718400-160726000	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:160718400-160731000	Weak transcription	Esophagus	oesophagus
6	chr1:160719400-160731200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:160720800-160725800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:160720800-160731600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:160721000-160724600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:160721200-160725600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:160721400-160725400	Weak transcription	Spleen	Spleen
12	chr1:160722000-160736400	Weak transcription	Primary T cells from cord blood	blood
13	chr1:160723000-160723800	Enhancers	Ovary	ovary
14	chr1:160723000-160724200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:160723000-160725800	Weak transcription	Fetal Thymus	thymus
16	chr1:160723000-160730000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:160723400-160725400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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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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