Variant report

Variant	rs9998686
Chromosome Location	chr4:15486798-15486799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15486404..15488431-chr4:15495017..15497202,2	K562	blood:
2	chr4:15484757..15487117-chr4:15489258..15491846,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1058412	0.81[CEU][hapmap]
rs11728800	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12500458	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs13131700	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1861048	1.00[CEU][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1861049	0.83[JPT][hapmap]
rs1861050	0.83[JPT][hapmap]
rs2080176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087622	0.83[EUR][1000 genomes]
rs34465372	0.84[EUR][1000 genomes]
rs4063953	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140934	0.94[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698112	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698386	0.81[AMR][1000 genomes]
rs4698387	0.84[EUR][1000 genomes]
rs4698395	0.81[CEU][hapmap]
rs6810461	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6836616	0.83[JPT][hapmap]
rs719993	0.84[YRI][hapmap]
rs7675761	0.81[CEU][hapmap]
rs9990934	0.81[YRI][hapmap]
rs9993748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998697	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9998686	CPEB2	cis	cerebellum	SCAN
rs9998686	FBXL5	cis	multi-tissue	Pritchard

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481600-15488000	Weak transcription	HSMMtube	muscle
2	chr4:15481600-15490200	Weak transcription	Esophagus	oesophagus
3	chr4:15481600-15498600	Weak transcription	Liver	Liver
4	chr4:15481600-15519000	Weak transcription	Gastric	stomach
5	chr4:15481800-15488200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:15482000-15487000	Weak transcription	HSMM	muscle
7	chr4:15482000-15487600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:15482000-15489600	Weak transcription	Brain Substantia Nigra	brain
9	chr4:15482000-15491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:15482000-15491800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:15482200-15487600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:15482200-15490400	Weak transcription	A549	lung
13	chr4:15482200-15519800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:15482400-15486800	Weak transcription	Fetal Brain Male	brain
15	chr4:15482400-15489600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:15482600-15486800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:15482600-15487400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:15482600-15487600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:15482600-15487600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr4:15482600-15516600	Weak transcription	Brain Angular Gyrus	brain
21	chr4:15482600-15526400	Weak transcription	HMEC	breast
22	chr4:15482800-15489600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:15482800-15518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:15483000-15490200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:15483200-15487400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:15483600-15493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:15483600-15498600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:15484800-15486800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:15484800-15490000	Weak transcription	Osteobl	bone
30	chr4:15485000-15486800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:15485000-15487800	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:15485000-15487800	Weak transcription	Fetal Intestine Large	intestine
33	chr4:15485000-15490200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:15485000-15490200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr4:15485000-15490200	Weak transcription	Fetal Intestine Small	intestine
36	chr4:15485000-15490200	Weak transcription	Lung	lung
37	chr4:15485000-15504800	Weak transcription	Ovary	ovary
38	chr4:15485200-15486800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:15485200-15494400	Weak transcription	Fetal Heart	heart
40	chr4:15485600-15489800	Weak transcription	NHLF	lung
41	chr4:15485800-15487000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:15485800-15487800	Strong transcription	Fetal Lung	lung
43	chr4:15486000-15486800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:15486200-15488200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:15486200-15490200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:15486200-15490200	Weak transcription	Aorta	Aorta
47	chr4:15486200-15490200	Weak transcription	Fetal Stomach	stomach
48	chr4:15486200-15490200	Weak transcription	Left Ventricle	heart
49	chr4:15486400-15486800	ZNF genes & repeats	Brain Anterior Caudate	brain
50	chr4:15486400-15487000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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