Variant report

Variant	rs2618479
Chromosome Location	chr8:11355821-11355822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13256690	0.83[ASN][1000 genomes]
rs13277113	0.89[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1478887	0.88[ASN][1000 genomes]
rs1478895	0.83[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1478900	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1478901	0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1531577	0.84[ASN][1000 genomes]
rs1564267	0.94[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs17153280	1.00[YRI][hapmap]
rs17153385	1.00[MEX][hapmap]
rs2244234	0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs2250412	0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2250788	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2251056	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2254546	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2254660	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2254891	0.87[ASN][1000 genomes]
rs2618455	0.83[ASW][hapmap];1.00[MEX][hapmap]
rs2618476	0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs2618478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618480	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2618481	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2736335	0.86[ASN][1000 genomes]
rs2736343	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2736344	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2736345	0.88[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2736354	1.00[MEX][hapmap]
rs2736360	0.85[MEX][hapmap]
rs35393613	0.80[ASN][1000 genomes]
rs4840565	0.87[ASN][1000 genomes]
rs4840568	0.89[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs62489069	0.80[ASN][1000 genomes]
rs7014565	0.85[MEX][hapmap]
rs7812879	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs922483	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9693589	0.82[ASN][1000 genomes]
rs9694294	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs998682	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs998683	0.89[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022074	chr8:11292256-11394526	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2618479	FAM167A	cis	lymphoblastoid	seeQTL
rs2618479	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11350200-11356600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr8:11352200-11360400	Weak transcription	Spleen	Spleen
3	chr8:11352600-11356200	Flanking Active TSS	Dnd41	blood
4	chr8:11352800-11357600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr8:11353200-11361000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr8:11353400-11357200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
7	chr8:11353400-11367200	Enhancers	Fetal Thymus	thymus
8	chr8:11353800-11357800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr8:11354000-11357200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr8:11354000-11357200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr8:11354000-11357200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr8:11354000-11357600	Enhancers	Thymus	Thymus
13	chr8:11354200-11356000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
14	chr8:11354200-11356000	Enhancers	NHEK	skin
15	chr8:11354200-11357200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:11354200-11357400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr8:11354400-11356600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr8:11354400-11356600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr8:11354400-11356600	Weak transcription	NHDF-Ad	bronchial
20	chr8:11354400-11356800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr8:11354400-11356800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr8:11354400-11357200	Weak transcription	NHLF	lung
23	chr8:11354400-11357400	Enhancers	Primary T cells from cord blood	blood
24	chr8:11354400-11357400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr8:11354400-11357400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr8:11354400-11357600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr8:11354600-11356200	Genic enhancers	Primary B cells from peripheral blood	blood
28	chr8:11354600-11356600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr8:11354800-11356400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr8:11354800-11356400	Weak transcription	Osteobl	bone
31	chr8:11354800-11356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr8:11354800-11356600	Weak transcription	HSMMtube	muscle
33	chr8:11354800-11356800	Weak transcription	NH-A	brain
34	chr8:11355000-11356000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr8:11355000-11356400	Weak transcription	HSMM	muscle
36	chr8:11355400-11357000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr8:11355400-11357000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:11355600-11356600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr8:11355600-11356600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr8:11355600-11356800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr8:11355800-11359200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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