Variant report

Variant	rs6980978
Chromosome Location	chr8:11274554-11274555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11273893..11276099-chr8:11313214..11316137,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10097252	0.86[ASN][1000 genomes]
rs10098597	0.89[ASN][1000 genomes]
rs10099353	0.89[ASN][1000 genomes]
rs11250135	0.83[ASN][1000 genomes]
rs12156245	1.00[CHB][hapmap]
rs13275905	0.89[ASN][1000 genomes]
rs6980803	0.89[ASN][1000 genomes]
rs6982763	0.89[ASN][1000 genomes]
rs7000458	0.81[ASN][1000 genomes]
rs7000625	0.89[ASN][1000 genomes]
rs7017797	0.89[ASN][1000 genomes]
rs7018324	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7836059	0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6980978	PRSS55	cis	cerebellum	SCAN
rs6980978	CTSB	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11269200-11275600	Enhancers	Fetal Thymus	thymus
2	chr8:11269400-11287400	Weak transcription	Right Atrium	heart
3	chr8:11269800-11274600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:11269800-11274800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:11269800-11275400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:11269800-11279800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:11270000-11279200	Weak transcription	Brain Anterior Caudate	brain
8	chr8:11270200-11274600	Weak transcription	Brain Substantia Nigra	brain
9	chr8:11270800-11275200	Enhancers	Primary B cells from peripheral blood	blood
10	chr8:11271000-11275200	Enhancers	Primary B cells from cord blood	blood
11	chr8:11271600-11274800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr8:11271600-11275200	Weak transcription	Brain Hippocampus Middle	brain
13	chr8:11271600-11291000	Weak transcription	Pancreas	Pancrea
14	chr8:11271800-11275400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr8:11273000-11286800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:11273000-11287000	Weak transcription	NHEK	skin
17	chr8:11273200-11275400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:11273200-11275400	Weak transcription	Osteobl	bone
19	chr8:11273200-11278000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr8:11273200-11279200	Weak transcription	HSMM	muscle
21	chr8:11273400-11275600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:11273800-11275400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr8:11273800-11276400	Enhancers	Thymus	Thymus
24	chr8:11274000-11275400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr8:11274000-11275600	Enhancers	Stomach Mucosa	stomach
26	chr8:11274000-11281600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr8:11274200-11275800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr8:11274200-11276600	Enhancers	Primary hematopoietic stem cells	blood
29	chr8:11274200-11276600	Enhancers	Gastric	stomach
30	chr8:11274400-11274600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr8:11274400-11274600	Enhancers	Brain Cingulate Gyrus	brain
32	chr8:11274400-11274800	Enhancers	Spleen	Spleen
33	chr8:11274400-11275200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr8:11274400-11276800	Flanking Active TSS	GM12878-XiMat	blood
35	chr8:11274400-11277000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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