Variant report

Variant	rs6810461
Chromosome Location	chr4:15482809-15482810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15481667..15484454-chr4:15772642..15775403,2	MCF-7	breast:
2	chr4:15475920..15478825-chr4:15482712..15485003,2	MCF-7	breast:
3	chr4:15480883..15483744-chr4:15651050..15653259,2	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];0.82[EUR][1000 genomes]
rs12500458	0.82[EUR][1000 genomes]
rs13131700	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1861048	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.85[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];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2080177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087622	0.84[EUR][1000 genomes]
rs34465372	0.85[EUR][1000 genomes]
rs4063953	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4140934	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698386	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4698387	0.85[EUR][1000 genomes]
rs4698395	0.81[CEU][hapmap]
rs6836616	0.83[JPT][hapmap]
rs719993	0.84[YRI][hapmap]
rs7675761	0.81[CEU][hapmap]
rs9990934	0.88[YRI][hapmap]
rs9993748	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9998686	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]
rs9998697	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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
rs6810461	FBXL5	cis	multi-tissue	Pritchard
rs6810461	CPEB2	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481200-15485200	Weak transcription	Right Ventricle	heart
2	chr4:15481400-15486200	Weak transcription	Spleen	Spleen
3	chr4:15481600-15484000	Weak transcription	Aorta	Aorta
4	chr4:15481600-15484200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:15481600-15484400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:15481600-15484400	Weak transcription	Placenta	Placenta
7	chr4:15481600-15484400	Weak transcription	K562	blood
8	chr4:15481600-15484600	Weak transcription	Right Atrium	heart
9	chr4:15481600-15488000	Weak transcription	HSMMtube	muscle
10	chr4:15481600-15490200	Weak transcription	Esophagus	oesophagus
11	chr4:15481600-15498600	Weak transcription	Liver	Liver
12	chr4:15481600-15519000	Weak transcription	Gastric	stomach
13	chr4:15481800-15483200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:15481800-15483200	Weak transcription	Fetal Kidney	kidney
15	chr4:15481800-15484000	Weak transcription	Ovary	ovary
16	chr4:15481800-15488200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:15482000-15483200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:15482000-15484000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:15482000-15484200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:15482000-15485400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:15482000-15486400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:15482000-15486600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:15482000-15487000	Weak transcription	HSMM	muscle
24	chr4:15482000-15487600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:15482000-15489600	Weak transcription	Brain Substantia Nigra	brain
26	chr4:15482000-15491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:15482000-15491800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:15482200-15484000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:15482200-15484600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:15482200-15484600	Weak transcription	NHEK	skin
31	chr4:15482200-15485000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:15482200-15485000	Strong transcription	Fetal Intestine Small	intestine
33	chr4:15482200-15486200	Strong transcription	Fetal Stomach	stomach
34	chr4:15482200-15486400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:15482200-15486600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:15482200-15487600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:15482200-15490400	Weak transcription	A549	lung
38	chr4:15482200-15519800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:15482400-15483000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:15482400-15483200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:15482400-15483400	Strong transcription	Lung	lung
42	chr4:15482400-15483400	Weak transcription	NHDF-Ad	bronchial
43	chr4:15482400-15483600	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:15482400-15484600	Weak transcription	Fetal Brain Female	brain
45	chr4:15482400-15484800	Weak transcription	Fetal Lung	lung
46	chr4:15482400-15485000	Strong transcription	Fetal Intestine Large	intestine
47	chr4:15482400-15485200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:15482400-15485200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:15482400-15485600	Weak transcription	HepG2	liver
50	chr4:15482400-15486000	Weak transcription	Brain Anterior Caudate	brain

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