Variant report

Variant	rs4129967
Chromosome Location	chr5:17000364-17000365
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16999937..17003903-chr5:17005517..17010107,4	MCF-7	breast:
2	chr5:16995098..16996958-chr5:17000346..17002199,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10070446	0.89[ASN][1000 genomes]
rs10074279	0.95[ASN][1000 genomes]
rs11133869	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11749259	0.95[ASN][1000 genomes]
rs11948777	0.95[ASN][1000 genomes]
rs11949513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11949968	0.83[ASN][1000 genomes]
rs11952906	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11959127	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12656631	0.93[ASN][1000 genomes]
rs13180256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13181713	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1806622	0.95[ASN][1000 genomes]
rs1909726	0.93[ASN][1000 genomes]
rs2402337	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35525756	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4360041	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4370273	0.83[ASN][1000 genomes]
rs4701673	0.95[ASN][1000 genomes]
rs4701674	0.93[ASN][1000 genomes]
rs4701675	0.93[ASN][1000 genomes]
rs4701676	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4701677	0.93[ASN][1000 genomes]
rs4702184	0.93[ASN][1000 genomes]
rs4702187	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58370320	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62369738	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62369739	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6873589	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6875279	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6877901	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7709189	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7714749	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7727270	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7732829	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7733016	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7734046	0.95[ASN][1000 genomes]
rs904753	0.95[ASN][1000 genomes]
rs954604	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3510797	chr5:16966764-17125849	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3510798	chr5:16966764-17125849	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1795984	chr5:16973769-17078295	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv597311	chr5:16980857-17012775	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1793716	chr5:16989318-17019351	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1794754	chr5:16993278-17012775	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1798338	chr5:16993278-17012775	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1802802	chr5:16993278-17012775	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3470358	chr5:16998712-17012413	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv3470359	chr5:16998712-17012413	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv15389	chr5:16999166-17012826	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1798573	chr5:17000364-17007689	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv1802645	chr5:17000364-17007689	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv1795581	chr5:17000364-17012775	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1796695	chr5:17000364-17012775	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv1799153	chr5:17000364-17012775	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv1799417	chr5:17000364-17012775	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv1802067	chr5:17000364-17012775	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	esv1802158	chr5:17000364-17012775	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv1796588	chr5:17000364-17033610	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4129967	FBXL7	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16995200-17000400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:16995400-17007200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:16995600-17000600	Weak transcription	HMEC	breast
4	chr5:16995600-17000600	Weak transcription	NHDF-Ad	bronchial
5	chr5:16995800-17000600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:16995800-17000800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:16995800-17000800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:16995800-17000800	Weak transcription	HSMM	muscle
9	chr5:16996000-17000400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:16996000-17000600	Weak transcription	NH-A	brain
11	chr5:16998800-17001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:16999600-17000400	Enhancers	A549	lung
13	chr5:16999600-17000600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:16999600-17006600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:16999800-17000600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:16999800-17001800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:16999800-17002200	Enhancers	NHLF	lung
18	chr5:17000000-17000600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:17000000-17001200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:17000000-17001400	Enhancers	HUVEC	blood vessel
21	chr5:17000000-17001400	Enhancers	NHEK	skin
22	chr5:17000000-17001600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:17000200-17000600	Enhancers	Osteobl	bone
24	chr5:17000200-17000800	Enhancers	HSMMtube	muscle
25	chr5:17000200-17001000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:17000200-17001800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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