Variant report

Variant	rs11959119
Chromosome Location	chr5:92937146-92937147
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:92925322..92926942-chr5:92936051..92937789,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1004941	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1046217	0.93[CEU][hapmap]
rs10514376	0.93[CEU][hapmap]
rs12186878	0.86[CEU][hapmap]
rs17083264	0.81[AMR][1000 genomes]
rs17083278	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs2279473	0.91[EUR][1000 genomes]
rs6556829	0.86[CEU][hapmap]
rs6884138	0.93[CEU][hapmap]
rs7712388	0.93[CEU][hapmap]
rs7721168	0.93[CEU][hapmap]
rs7721509	1.00[CEU][hapmap]
rs7736624	0.93[CEU][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451945	chr5:92858750-93024740	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv830404	chr5:92868336-93048257	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv1819334	chr5:92892591-92956733	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv823130	chr5:92896346-92966016	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv4918	chr5:92898426-92943359	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv823132	chr5:92898512-92969668	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv532196	chr5:92933949-93573527	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11959119	GPR150	cis	cerebellum	SCAN
rs11959119	CETN3	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92929600-92937800	Weak transcription	Right Atrium	heart
2	chr5:92932800-92937800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:92932800-92938200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:92934000-92938400	Bivalent/Poised TSS	Fetal Brain Female	brain
5	chr5:92934800-92938800	Flanking Active TSS	NH-A	brain
6	chr5:92935200-92937200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:92935200-92939000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:92935200-92939600	Weak transcription	Gastric	stomach
9	chr5:92935400-92937400	Bivalent/Poised TSS	Fetal Brain Male	brain
10	chr5:92935400-92939400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:92935400-92939600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:92935400-92939600	Weak transcription	Ovary	ovary
13	chr5:92935400-92939600	Weak transcription	Pancreas	Pancrea
14	chr5:92936000-92937200	Flanking Active TSS	Fetal Kidney	kidney
15	chr5:92936000-92937200	Flanking Active TSS	NHLF	lung
16	chr5:92936000-92938800	Bivalent Enhancer	Fetal Stomach	stomach
17	chr5:92936200-92937400	Bivalent Enhancer	NHDF-Ad	bronchial
18	chr5:92936600-92938000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:92936600-92938600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr5:92936800-92937200	Bivalent Enhancer	Fetal Lung	lung
21	chr5:92936800-92937600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr5:92936800-92937600	Weak transcription	Brain Germinal Matrix	brain
23	chr5:92937000-92937600	Enhancers	Hela-S3	cervix
24	chr5:92937000-92938000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:92937000-92938600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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