Variant report

Variant	rs2898279
Chromosome Location	chr8:11295251-11295252
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11291994..11295873-chr8:11300373..11305945,6	K562	blood:
2	chr8:11294217..11296027-chr8:11297947..11300867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154319	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10088323	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10102600	0.84[JPT][hapmap]
rs10448145	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs10481455	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10503423	0.85[CHB][hapmap]
rs1057750	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10903338	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11250138	0.82[CHB][hapmap]
rs11779875	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11782375	0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11785710	0.83[ASN][1000 genomes]
rs12114115	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12543308	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12549796	0.85[CHB][hapmap]
rs12674532	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs13259219	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]
rs13264212	0.86[CHB][hapmap]
rs13439411	0.85[CHB][hapmap]
rs2001463	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2003423	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs2280803	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2409766	0.89[ASN][1000 genomes]
rs2409767	0.80[ASN][1000 genomes]
rs2409771	0.80[ASN][1000 genomes]
rs2409772	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2409773	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2409775	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2618431	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2618475	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2736320	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs28639872	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898280	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs35433745	0.81[EUR][1000 genomes]
rs4240675	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4581006	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4840561	0.85[ASN][1000 genomes]
rs4841529	0.89[JPT][hapmap]
rs4841530	0.90[CHB][hapmap]
rs4841537	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4841539	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4841540	0.82[ASN][1000 genomes]
rs6601592	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6982606	0.95[CHB][hapmap]
rs6984212	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6998387	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7001675	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7003814	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7007712	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7018402	0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7830445	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7846252	0.90[CHB][hapmap]
rs9644687	0.86[CHB][hapmap]
rs9693089	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9792175	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9792375	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9792397	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[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
rs2898279	FAM167A	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:37 , 50 per page) page: 1

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	chr8:11286600-11296200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr8:11287400-11296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr8:11287400-11296400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:11287400-11297600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:11287800-11300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr8:11287800-11300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:11287800-11313600	Weak transcription	Right Atrium	heart
11	chr8:11288000-11297600	Weak transcription	HSMM	muscle
12	chr8:11288200-11300200	Weak transcription	Brain Hippocampus Middle	brain
13	chr8:11289000-11295400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:11289000-11295600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:11289800-11299600	Weak transcription	Brain Anterior Caudate	brain
16	chr8:11289800-11305800	Weak transcription	Osteobl	bone
17	chr8:11291200-11296200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr8:11291600-11296200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr8:11291600-11303800	Weak transcription	Brain Angular Gyrus	brain
20	chr8:11291800-11300800	Weak transcription	NHEK	skin
21	chr8:11292200-11296000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr8:11292400-11313000	Weak transcription	Pancreas	Pancrea
23	chr8:11292600-11296400	Weak transcription	Thymus	Thymus
24	chr8:11292600-11302200	Weak transcription	Lung	lung
25	chr8:11292800-11297400	Weak transcription	Gastric	stomach
26	chr8:11293800-11297200	Weak transcription	Right Ventricle	heart
27	chr8:11294000-11295400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr8:11294000-11296400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr8:11294000-11297000	Weak transcription	Fetal Heart	heart
30	chr8:11294200-11296200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:11294400-11295400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr8:11295000-11296200	Weak transcription	Brain Substantia Nigra	brain
33	chr8:11295000-11296200	Weak transcription	Fetal Thymus	thymus
34	chr8:11295000-11298000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr8:11295200-11295600	Enhancers	H9 Cell Line	embryonic stem cell
36	chr8:11295200-11297000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr8:11295200-11298400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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