Variant report

Variant	rs13259219
Chromosome Location	chr8:11297277-11297278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10088323	0.82[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs10102600	0.85[JPT][hapmap]
rs10448145	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10481455	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs10503423	0.85[CHB][hapmap]
rs1057750	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10903338	0.80[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11779875	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs11782375	0.90[CHB][hapmap]
rs11785710	0.83[ASN][1000 genomes]
rs12114115	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12543308	0.81[CHB][hapmap]
rs12549796	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12674532	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs13264212	0.81[CHB][hapmap]
rs13439411	0.80[CHB][hapmap]
rs2001463	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2003422	0.81[ASN][1000 genomes]
rs2003423	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2280803	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2409766	0.89[ASN][1000 genomes]
rs2409767	0.80[ASN][1000 genomes]
rs2409771	0.80[ASN][1000 genomes]
rs2618431	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2618475	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs2736320	0.81[CHB][hapmap]
rs28639872	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898279	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898280	0.81[CHB][hapmap]
rs35433745	0.82[EUR][1000 genomes]
rs4240675	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4581006	0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4840561	0.85[ASN][1000 genomes]
rs4841529	0.90[JPT][hapmap]
rs4841530	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4841539	0.81[CHB][hapmap]
rs4841540	0.82[ASN][1000 genomes]
rs6601592	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs6982606	0.91[CHB][hapmap]
rs6984212	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6998387	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7001675	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7003814	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7007712	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7018402	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7830445	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7846252	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs9644687	0.81[CHB][hapmap]
rs9693089	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9792227	0.80[ASN][1000 genomes]
rs9792375	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs9792397	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	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
7	nsv470183	chr8:11236975-11307118	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv465465	chr8:11245064-11307118	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv610275	chr8:11245064-11307118	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv522860	chr8:11253879-11330364	Bivalent/Poised TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv890357	chr8:11286146-11330364	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1030756	chr8:11292073-11332782	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13259219	FAM167A	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11280600-11308800	Weak transcription	Primary B cells from cord blood	blood
2	chr8:11280800-11297600	Weak transcription	Spleen	Spleen
3	chr8:11286200-11306400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:11287400-11297600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:11287800-11300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr8:11287800-11300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:11287800-11313600	Weak transcription	Right Atrium	heart
8	chr8:11288000-11297600	Weak transcription	HSMM	muscle
9	chr8:11288200-11300200	Weak transcription	Brain Hippocampus Middle	brain
10	chr8:11289800-11299600	Weak transcription	Brain Anterior Caudate	brain
11	chr8:11289800-11305800	Weak transcription	Osteobl	bone
12	chr8:11291600-11303800	Weak transcription	Brain Angular Gyrus	brain
13	chr8:11291800-11300800	Weak transcription	NHEK	skin
14	chr8:11292400-11313000	Weak transcription	Pancreas	Pancrea
15	chr8:11292600-11302200	Weak transcription	Lung	lung
16	chr8:11292800-11297400	Weak transcription	Gastric	stomach
17	chr8:11295000-11298000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr8:11295200-11298400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr8:11295400-11298200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:11295400-11298200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:11295400-11298400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr8:11295400-11298400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr8:11295400-11298800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:11295400-11299200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr8:11295400-11299800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr8:11295600-11298200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr8:11295600-11298200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr8:11295800-11298200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr8:11296000-11300600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:11296200-11298200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr8:11296200-11298200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:11296200-11305800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr8:11296200-11319200	Enhancers	Fetal Thymus	thymus
34	chr8:11296400-11298000	Enhancers	Thymus	Thymus
35	chr8:11296400-11298200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr8:11296400-11301800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr8:11296800-11298000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:11296800-11298200	Bivalent Enhancer	Placenta	Placenta
39	chr8:11296800-11298400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr8:11296800-11299000	Enhancers	GM12878-XiMat	blood
41	chr8:11297000-11297600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr8:11297000-11297800	Enhancers	HSMMtube	muscle
43	chr8:11297000-11298000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr8:11297000-11298200	Enhancers	Fetal Heart	heart
45	chr8:11297000-11298800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:11297000-11299000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr8:11297000-11299600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr8:11297000-11300400	Weak transcription	Brain Substantia Nigra	brain
49	chr8:11297200-11297800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr8:11297200-11297800	Enhancers	Right Ventricle	heart

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