Variant report

Variant	rs2518564
Chromosome Location	chr1:159062436-159062437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159062221..159063748-chr1:159065497..159068342,2	K562	blood:
2	chr1:159057678..159060564-chr1:159061806..159064671,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1057027	0.81[GIH][hapmap]
rs1057028	0.83[GIH][hapmap]
rs1101998	0.83[GIH][hapmap]
rs12094741	0.81[GIH][hapmap]
rs12124059	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs1633256	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs1633266	0.80[JPT][hapmap]
rs1772407	0.86[CHD][hapmap]
rs1772408	0.86[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs1772414	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs1772415	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs1894043	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2078723	0.90[ASN][1000 genomes]
rs2518562	0.89[GIH][hapmap]
rs2518563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518565	0.90[ASN][1000 genomes]
rs2570916	0.89[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs2814757	0.86[ASN][1000 genomes]
rs2814759	0.90[ASN][1000 genomes]
rs2814760	0.90[ASN][1000 genomes]
rs2814764	1.00[ASN][1000 genomes]
rs2852723	0.90[ASN][1000 genomes]
rs855865	0.92[GIH][hapmap];0.85[TSI][hapmap]
rs855866	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855867	0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs855871	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs856046	0.92[AFR][1000 genomes]
rs856055	0.83[GIH][hapmap]
rs861318	0.83[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2518564	AIM2	Cis_1M	lymphoblastoid	RTeQTL
rs2518564	IFI16	cis	parietal	SCAN
rs2518564	AIM2	cis	lymphoblastoid	seeQTL
rs2518564	TMEM79	cis	parietal	SCAN
rs2518564	IFI16	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159051200-159063400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:159056200-159063400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:159057400-159062800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:159057800-159062600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:159059400-159062600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:159060000-159062600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:159060400-159062600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:159060400-159062600	Enhancers	HSMM	muscle
9	chr1:159060400-159062800	Enhancers	HUVEC	blood vessel
10	chr1:159060600-159062600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:159060600-159062600	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:159060600-159062600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:159060800-159062600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:159061000-159062800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:159061400-159062600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:159061600-159062600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:159061600-159062600	Enhancers	Esophagus	oesophagus
18	chr1:159061600-159062600	Enhancers	NH-A	brain
19	chr1:159061800-159062600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:159061800-159062600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:159061800-159062600	Enhancers	NHDF-Ad	bronchial
22	chr1:159061800-159062600	Enhancers	Osteobl	bone
23	chr1:159061800-159063400	Enhancers	Hela-S3	cervix
24	chr1:159061800-159063400	Enhancers	HMEC	breast
25	chr1:159062200-159062600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr1:159062200-159062600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:159062400-159062600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:159062400-159062600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:159062400-159062600	Enhancers	NHLF	lung
30	chr1:159062400-159063200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:159062400-159063200	Enhancers	NHEK	skin
32	chr1:159062400-159064800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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