Variant report

Variant	rs6449146
Chromosome Location	chr4:15576264-15576265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10003739	0.82[ASN][1000 genomes]
rs10008376	0.86[JPT][hapmap];0.82[MKK][hapmap]
rs10008889	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10008975	0.86[JPT][hapmap];0.83[MKK][hapmap]
rs10020408	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs10022610	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10025837	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs10026851	0.82[ASN][1000 genomes]
rs10034328	0.82[ASN][1000 genomes]
rs10214	0.86[JPT][hapmap];0.83[MKK][hapmap]
rs10939621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939628	0.81[ASN][1000 genomes]
rs1134634	1.00[CHB][hapmap]
rs11932730	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs11943107	0.88[ASN][1000 genomes]
rs12640192	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs12645849	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12649803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651550	0.86[JPT][hapmap]
rs13104845	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13116304	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs13121363	0.88[ASN][1000 genomes]
rs13142069	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1473166	0.87[ASN][1000 genomes]
rs16892140	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs16892152	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs2041671	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs2110361	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2160044	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs28522268	0.83[ASN][1000 genomes]
rs28528670	0.86[ASN][1000 genomes]
rs28534607	0.87[ASN][1000 genomes]
rs28661857	0.82[ASN][1000 genomes]
rs3822298	0.87[ASN][1000 genomes]
rs4235380	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs4270584	0.86[JPT][hapmap];0.83[MKK][hapmap]
rs4280723	0.88[ASN][1000 genomes]
rs4280724	0.88[ASN][1000 genomes]
rs4393989	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4557256	0.86[JPT][hapmap];0.82[MKK][hapmap]
rs4583752	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs4591601	0.82[ASN][1000 genomes]
rs4631041	0.86[JPT][hapmap]
rs4698117	0.81[ASN][1000 genomes]
rs4698402	0.86[JPT][hapmap]
rs4698403	0.82[ASN][1000 genomes]
rs4698408	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs4698409	0.86[JPT][hapmap]
rs56041141	0.83[ASN][1000 genomes]
rs59055524	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60813847	0.84[ASN][1000 genomes]
rs62290565	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414765	0.86[JPT][hapmap]
rs6449147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449149	0.86[ASN][1000 genomes]
rs6449161	0.86[JPT][hapmap]
rs73125606	0.86[ASN][1000 genomes]
rs741180	0.88[ASN][1000 genomes]
rs7438356	0.86[JPT][hapmap]
rs759212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7661102	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs7665390	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs7665915	1.00[CHB][hapmap]
rs7682586	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7684446	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7685083	0.86[JPT][hapmap];0.82[MKK][hapmap]
rs7692607	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7696127	0.86[JPT][hapmap]
rs7697314	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872678	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs9996452	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6449146	FBXL5	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
2	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
4	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
5	chr4:15546000-15589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
7	chr4:15554600-15601400	Weak transcription	A549	lung
8	chr4:15555800-15589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
10	chr4:15559600-15579000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr4:15560200-15577400	Weak transcription	HSMMtube	muscle
12	chr4:15560200-15580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:15563600-15576600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:15564000-15600600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:15564400-15603200	Weak transcription	HMEC	breast
16	chr4:15564600-15603600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
18	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
19	chr4:15565600-15604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:15566200-15596800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:15566800-15580400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:15568400-15655600	Weak transcription	Gastric	stomach
25	chr4:15568600-15589400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:15569600-15588600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:15569600-15596400	Weak transcription	NHDF-Ad	bronchial
28	chr4:15569600-15603600	Weak transcription	Spleen	Spleen
29	chr4:15569600-15604200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:15570200-15601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:15570600-15577600	Weak transcription	Aorta	Aorta
32	chr4:15570600-15588200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:15570600-15602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:15570600-15602000	Weak transcription	Pancreas	Pancrea
35	chr4:15570800-15582000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:15570800-15588800	Weak transcription	Psoas Muscle	Psoas
37	chr4:15570800-15589600	Weak transcription	Lung	lung
38	chr4:15571000-15578200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:15571000-15597200	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:15571200-15577400	Weak transcription	Left Ventricle	heart
41	chr4:15571200-15588000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:15571200-15588800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:15571400-15596000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:15571800-15577400	Weak transcription	Placenta	Placenta
45	chr4:15571800-15585800	Weak transcription	Brain Anterior Caudate	brain
46	chr4:15572000-15576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:15572000-15593400	Weak transcription	Fetal Brain Male	brain
48	chr4:15572200-15576800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:15572200-15576800	Weak transcription	Fetal Intestine Large	intestine
50	chr4:15572200-15577400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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