Variant report

Variant	rs546757
Chromosome Location	chr1:160737621-160737622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11582702	0.87[EUR][1000 genomes]
rs12064520	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068654	0.88[EUR][1000 genomes]
rs12082740	0.88[EUR][1000 genomes]
rs1328111	0.87[EUR][1000 genomes]
rs2090755	0.81[EUR][1000 genomes]
rs2176873	0.88[EUR][1000 genomes]
rs477299	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495706	0.81[EUR][1000 genomes]
rs504170	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518242	0.88[EUR][1000 genomes]
rs518721	0.81[EUR][1000 genomes]
rs528095	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532466	0.81[EUR][1000 genomes]
rs563781	0.82[EUR][1000 genomes]
rs564833	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564883	0.87[EUR][1000 genomes]
rs569932	0.82[EUR][1000 genomes]
rs574491	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579821	0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs546757	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs546757	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160736400-160737800	Enhancers	Primary T cells from cord blood	blood
2	chr1:160736400-160737800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:160736400-160737800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:160736400-160737800	Enhancers	Dnd41	blood
5	chr1:160736400-160738200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:160736600-160737800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:160736600-160738200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:160736600-160738400	Enhancers	Fetal Thymus	thymus
9	chr1:160736800-160737800	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:160736800-160738400	Flanking Active TSS	GM12878-XiMat	blood
11	chr1:160736800-160740000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:160737000-160737800	Enhancers	K562	blood
13	chr1:160737200-160738200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:160737200-160738200	Enhancers	HMEC	breast
15	chr1:160737200-160738400	Flanking Active TSS	NHEK	skin
16	chr1:160737400-160738200	Enhancers	Primary B cells from cord blood	blood
17	chr1:160737400-160738200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:160737400-160738400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr1:160737600-160737800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr1:160737600-160737800	Active TSS	HepG2	liver
21	chr1:160737600-160738000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:160737600-160738000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr1:160737600-160738000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:160737600-160738000	Enhancers	Esophagus	oesophagus
25	chr1:160737600-160738000	Enhancers	Placenta	Placenta
26	chr1:160737600-160738000	Enhancers	Left Ventricle	heart
27	chr1:160737600-160738000	Enhancers	Spleen	Spleen
28	chr1:160737600-160738200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:160737600-160738200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:160737600-160738200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:160737600-160738200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr1:160737600-160738200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr1:160737600-160738200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:160737600-160738200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:160737600-160738200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:160737600-160738200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr1:160737600-160738200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr1:160737600-160738200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:160737600-160738200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:160737600-160738200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:160737600-160738200	Active TSS	Colonic Mucosa	Colon
42	chr1:160737600-160738200	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr1:160737600-160738200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr1:160737600-160738400	Enhancers	Ovary	ovary

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