Variant report

Variant	rs569932
Chromosome Location	chr1:160725854-160725855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11265473	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12064520	0.82[EUR][1000 genomes]
rs477299	0.81[EUR][1000 genomes]
rs489286	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs495706	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs504170	0.82[EUR][1000 genomes]
rs518721	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528095	0.82[EUR][1000 genomes]
rs546757	0.82[EUR][1000 genomes]
rs549103	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs564833	0.82[EUR][1000 genomes]
rs574491	0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs569932	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs569932	SLAMF7	cis	Lymphoblastoid	GTEx
rs569932	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs569932	SLAMF7	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 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	chr1:160718400-160726000	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr1:160718400-160731000	Weak transcription	Esophagus	oesophagus
4	chr1:160719400-160731200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:160720800-160731600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:160722000-160736400	Weak transcription	Primary T cells from cord blood	blood
7	chr1:160723000-160730000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:160724200-160727800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:160724400-160730000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:160725400-160727200	Enhancers	GM12878-XiMat	blood
11	chr1:160725400-160727800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:160725600-160727200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:160725800-160726000	Enhancers	Duodenum Mucosa	Duodenum
14	chr1:160725800-160726400	Enhancers	Fetal Thymus	thymus

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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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