Variant report

Variant	rs28394730
Chromosome Location	chr4:15665272-15665273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:15664452-15666087	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:15664444..15667043-chr4:15668246..15669921,2	K562	blood:
2	chr4:15663938..15667635-chr4:15670287..15673065,4	K562	blood:
3	chr4:15655910..15661308-chr4:15665213..15668611,5	K562	blood:
4	chr4:15662285..15665284-chr4:15678264..15680948,2	MCF-7	breast:
5	chr4:15659405..15662406-chr4:15663977..15668803,5	MCF-7	breast:
6	chr4:15654775..15659231-chr4:15659761..15666940,9	K562	blood:
7	chr4:15664653..15666973-chr4:15669930..15673591,3	MCF-7	breast:

No data

Variant related genes	Relation type
FBXL5	TF binding region
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10005305	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10008878	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10015827	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10017222	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10025875	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10034315	0.91[AFR][1000 genomes]
rs10433813	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722300	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11722854	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723478	0.97[AFR][1000 genomes]
rs11729955	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730088	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11732953	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12642407	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12650529	0.89[AFR][1000 genomes]
rs13134177	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13150957	0.97[AFR][1000 genomes]
rs17405811	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1786	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28402170	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28447067	0.97[AFR][1000 genomes]
rs28604503	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28644177	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28820655	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34473224	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34559117	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35013326	0.96[AFR][1000 genomes]
rs3756247	0.81[ASN][1000 genomes]
rs3775956	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775957	0.97[AFR][1000 genomes]
rs4301111	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4331772	0.91[AFR][1000 genomes]
rs4346644	0.97[AFR][1000 genomes]
rs4396986	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4423870	0.86[AFR][1000 genomes]
rs4484296	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4549375	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4554069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600905	0.91[AFR][1000 genomes]
rs4698116	0.91[AFR][1000 genomes]
rs6414764	0.97[AFR][1000 genomes]
rs6449152	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815254	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6815296	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6816982	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6823775	0.89[AFR][1000 genomes]
rs6824422	0.89[AFR][1000 genomes]
rs6825051	0.81[AFR][1000 genomes]
rs6826058	0.97[AFR][1000 genomes]
rs6827406	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6828776	0.87[AFR][1000 genomes]
rs6839654	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6843740	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6848779	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6852735	0.87[AFR][1000 genomes]
rs6857442	0.95[AFR][1000 genomes]
rs7434484	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667175	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7698596	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9994518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28394730	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15657600-15681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:15657800-15666800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:15657800-15667800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:15658000-15665400	Weak transcription	Psoas Muscle	Psoas
5	chr4:15658000-15666800	Weak transcription	Thymus	Thymus
6	chr4:15658000-15667400	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:15658000-15667800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:15658000-15672200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:15658000-15673800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:15658200-15666600	Weak transcription	HUVEC	blood vessel
14	chr4:15658200-15666800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:15658200-15667200	Weak transcription	Fetal Thymus	thymus
16	chr4:15658200-15667400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:15658200-15667400	Weak transcription	NH-A	brain
18	chr4:15658200-15667800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:15658200-15667800	Weak transcription	NHLF	lung
20	chr4:15658200-15668000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:15658200-15670600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:15658200-15679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:15658200-15679200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach
25	chr4:15658400-15667000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:15658400-15667400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:15658400-15668400	Weak transcription	Dnd41	blood
28	chr4:15658400-15668600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:15658600-15673000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:15658600-15679000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:15659600-15668200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:15659800-15678600	Weak transcription	K562	blood
33	chr4:15660000-15667400	Weak transcription	HSMMtube	muscle
34	chr4:15660000-15667400	Weak transcription	NHDF-Ad	bronchial
35	chr4:15660000-15668600	Weak transcription	HepG2	liver
36	chr4:15660200-15665800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:15660200-15670600	Weak transcription	Fetal Lung	lung
38	chr4:15660400-15679200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:15661200-15668000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:15661400-15667400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:15661600-15667200	Weak transcription	A549	lung
42	chr4:15661600-15667600	Weak transcription	Osteobl	bone
43	chr4:15661600-15668400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:15661600-15668800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr4:15661600-15678600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:15661800-15667200	Weak transcription	HSMM	muscle
47	chr4:15662000-15667000	Weak transcription	Adipose Nuclei	Adipose
48	chr4:15662000-15667400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:15662000-15667400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:15662000-15668200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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