Variant report

Variant	rs2898280
Chromosome Location	chr8:11321292-11321293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11319006..11321957-chr8:11323524..11325949,2	MCF-7	breast:
2	chr8:11312570..11318244-chr8:11320573..11323970,6	K562	blood:
3	chr8:11319355..11321594-chr8:11322106..11323740,2	K562	blood:

Variant related genes	Relation type
ENSG00000154319	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10088323	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10102600	0.86[JPT][hapmap]
rs10448145	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10481455	0.81[JPT][hapmap]
rs10503423	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1057750	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10903338	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11250138	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11777505	0.81[ASN][1000 genomes]
rs11779875	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs11782375	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12543308	0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs12549796	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs12674532	0.81[JPT][hapmap]
rs13248746	0.81[ASN][1000 genomes]
rs13259219	0.81[CHB][hapmap]
rs13264212	0.91[CHB][hapmap];0.90[CHD][hapmap]
rs13439411	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs2003423	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs2280803	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2409772	0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap]
rs2409773	0.95[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2409775	0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap]
rs2618431	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2618475	0.81[CHB][hapmap]
rs2736320	0.82[CHB][hapmap]
rs2898279	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs34801597	0.84[ASN][1000 genomes]
rs4240675	0.81[CHB][hapmap]
rs4581006	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4841529	0.81[JPT][hapmap]
rs4841530	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4841537	0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs4841539	0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs4841540	0.81[CHD][hapmap]
rs58004460	0.81[ASN][1000 genomes]
rs6601592	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs6982606	0.82[CHB][hapmap]
rs6984212	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6998387	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7001675	0.86[CHB][hapmap]
rs7007712	0.82[CHB][hapmap]
rs7846252	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9644687	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9693089	0.91[CHB][hapmap]
rs9792175	0.95[CHB][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap]
rs9792375	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	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
rs2898280	FAM167A	cis	Skin Sun Exposed Lower leg	GTEx
rs2898280	FAM167A	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11303600-11323200	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr8:11307200-11322000	Weak transcription	HSMMtube	muscle
3	chr8:11313400-11323000	Enhancers	Primary B cells from cord blood	blood
4	chr8:11314200-11323200	Weak transcription	Right Atrium	heart
5	chr8:11315400-11323000	Enhancers	Primary B cells from peripheral blood	blood
6	chr8:11315600-11321600	Weak transcription	Spleen	Spleen
7	chr8:11315600-11322800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:11316000-11322800	Enhancers	GM12878-XiMat	blood
9	chr8:11316400-11323400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr8:11317000-11323000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr8:11317200-11322000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr8:11317200-11322000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr8:11317200-11322000	Weak transcription	Fetal Heart	heart
14	chr8:11317600-11321800	Enhancers	Brain Anterior Caudate	brain
15	chr8:11318000-11321400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:11318600-11322400	Enhancers	Fetal Brain Female	brain
17	chr8:11318800-11321400	Weak transcription	Fetal Kidney	kidney
18	chr8:11318800-11322000	Enhancers	Brain Cingulate Gyrus	brain
19	chr8:11319000-11322400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr8:11319200-11322800	Weak transcription	A549	lung
21	chr8:11319400-11321600	Weak transcription	Osteobl	bone
22	chr8:11319400-11323000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr8:11319400-11323200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:11319400-11323600	Enhancers	Gastric	stomach
25	chr8:11319600-11321800	Weak transcription	Fetal Lung	lung
26	chr8:11319800-11321600	Weak transcription	Brain Angular Gyrus	brain
27	chr8:11319800-11321800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr8:11319800-11322800	Weak transcription	HSMM	muscle
29	chr8:11320000-11323200	Enhancers	Lung	lung
30	chr8:11320000-11323400	Enhancers	Pancreas	Pancrea
31	chr8:11320000-11323800	Enhancers	Liver	Liver
32	chr8:11320200-11321400	Weak transcription	Brain Hippocampus Middle	brain
33	chr8:11320200-11321600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr8:11320200-11322800	Enhancers	Brain Substantia Nigra	brain
35	chr8:11320400-11322600	Bivalent Enhancer	Stomach Mucosa	stomach
36	chr8:11320800-11321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr8:11320800-11321600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr8:11320800-11322000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr8:11320800-11322000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr8:11320800-11322600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr8:11320800-11322800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr8:11321000-11321600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr8:11321000-11321800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr8:11321000-11322600	Enhancers	Fetal Thymus	thymus
45	chr8:11321000-11323200	Enhancers	Colonic Mucosa	Colon
46	chr8:11321000-11323400	Bivalent Enhancer	Fetal Stomach	stomach
47	chr8:11321200-11321600	Genic enhancers	NHEK	skin
48	chr8:11321200-11322000	Enhancers	Fetal Brain Male	brain
49	chr8:11321200-11322800	Enhancers	Brain Germinal Matrix	brain
50	chr8:11321200-11323200	Bivalent Enhancer	Placenta	Placenta

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