Variant report

Variant	rs10939621
Chromosome Location	chr4:15578068-15578069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10003739	0.81[ASN][1000 genomes]
rs10008376	0.85[JPT][hapmap]
rs10008889	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs10008975	0.85[JPT][hapmap]
rs10020408	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs10022610	0.89[CHB][hapmap]
rs10025837	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10026851	0.81[ASN][1000 genomes]
rs10034328	0.81[ASN][1000 genomes]
rs10214	0.85[JPT][hapmap]
rs1134634	1.00[CHB][hapmap]
rs11932730	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11943107	0.87[ASN][1000 genomes]
rs12640192	1.00[CHB][hapmap]
rs12645849	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs12649803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651550	0.86[JPT][hapmap]
rs13104845	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13116304	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13121363	0.86[ASN][1000 genomes]
rs13142069	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1473166	0.86[ASN][1000 genomes]
rs16892140	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs16892152	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2041671	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2110361	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2160044	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs28522268	0.82[ASN][1000 genomes]
rs28528670	0.85[ASN][1000 genomes]
rs28534607	0.86[ASN][1000 genomes]
rs28661857	0.81[ASN][1000 genomes]
rs3822298	0.86[ASN][1000 genomes]
rs4235380	1.00[CHB][hapmap]
rs4270584	0.85[JPT][hapmap]
rs4280723	0.87[ASN][1000 genomes]
rs4280724	0.86[ASN][1000 genomes]
rs4393989	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs4557256	0.85[JPT][hapmap]
rs4583752	1.00[CHB][hapmap]
rs4591601	0.81[ASN][1000 genomes]
rs4631041	0.85[JPT][hapmap];0.81[YRI][hapmap]
rs4698402	0.85[JPT][hapmap]
rs4698403	0.81[ASN][1000 genomes]
rs4698408	1.00[CHB][hapmap]
rs4698409	0.85[JPT][hapmap]
rs56041141	0.82[ASN][1000 genomes]
rs59055524	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60813847	0.83[ASN][1000 genomes]
rs62290565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414765	0.85[JPT][hapmap]
rs6449146	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]
rs6449147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449149	0.85[ASN][1000 genomes]
rs6449161	0.85[JPT][hapmap]
rs73125606	0.84[ASN][1000 genomes]
rs741180	0.86[ASN][1000 genomes]
rs7438356	0.85[JPT][hapmap];0.82[YRI][hapmap]
rs759212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661102	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs7665390	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7665915	1.00[CHB][hapmap]
rs7682586	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs7684446	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7685083	0.85[JPT][hapmap]
rs7692607	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7696127	0.85[JPT][hapmap]
rs7697314	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs872678	1.00[CHB][hapmap]
rs9996452	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[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
rs10939621	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
3	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
4	chr4:15546000-15589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
6	chr4:15554600-15601400	Weak transcription	A549	lung
7	chr4:15555800-15589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
9	chr4:15559600-15579000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr4:15560200-15580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:15564000-15600600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:15564400-15603200	Weak transcription	HMEC	breast
13	chr4:15564600-15603600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
15	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
16	chr4:15565600-15604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:15566200-15596800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:15566800-15580400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:15568400-15655600	Weak transcription	Gastric	stomach
22	chr4:15568600-15589400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:15569600-15588600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:15569600-15596400	Weak transcription	NHDF-Ad	bronchial
25	chr4:15569600-15603600	Weak transcription	Spleen	Spleen
26	chr4:15569600-15604200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:15570200-15601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:15570600-15588200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:15570600-15602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:15570600-15602000	Weak transcription	Pancreas	Pancrea
31	chr4:15570800-15582000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:15570800-15588800	Weak transcription	Psoas Muscle	Psoas
33	chr4:15570800-15589600	Weak transcription	Lung	lung
34	chr4:15571000-15578200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr4:15571000-15597200	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:15571200-15588000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:15571200-15588800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:15571400-15596000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:15571800-15585800	Weak transcription	Brain Anterior Caudate	brain
40	chr4:15572000-15593400	Weak transcription	Fetal Brain Male	brain
41	chr4:15572200-15578400	Weak transcription	Liver	Liver
42	chr4:15572200-15578600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:15572200-15579200	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:15572200-15583200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:15572200-15585800	Weak transcription	Primary B cells from cord blood	blood
46	chr4:15572200-15586800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr4:15572200-15588200	Weak transcription	Adipose Nuclei	Adipose
48	chr4:15572200-15588600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:15572200-15591600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:15572200-15593600	Weak transcription	Brain Inferior Temporal Lobe	brain

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