Variant report

Variant	rs11722854
Chromosome Location	chr4:15680918-15680919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr4:15680899-15681030	K562	blood:	n/a	n/a
2	MYC	chr4:15680894-15681263	MCF10A-Er-Src	breast:	n/a	n/a
3	BHLHE40	chr4:15680783-15681149	K562	blood:	n/a	n/a
4	ZNF384	chr4:15680434-15681617	K562	blood:	n/a	chr4:15681349-15681357

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:15662285..15665284-chr4:15678264..15680948,2	MCF-7	breast:
2	chr4:15673240..15674969-chr4:15677739..15681015,3	MCF-7	breast:
3	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
4	chr4:15652080..15658606-chr4:15677363..15685579,17	MCF-7	breast:
5	chr4:15655595..15658742-chr4:15680185..15687360,10	MCF-7	breast:
6	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:

No data

Variant related genes	Relation type
FAM200B	TF binding region
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10005305	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10008878	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10015827	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10017222	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10025875	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10433813	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722300	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11729955	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730088	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11732953	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11947383	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12642407	0.81[ASN][1000 genomes]
rs13134177	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17405811	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1786	0.81[ASN][1000 genomes]
rs28394730	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402170	0.81[ASN][1000 genomes]
rs28604503	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28644177	0.81[ASN][1000 genomes]
rs28820655	0.81[ASN][1000 genomes]
rs34473224	0.81[ASN][1000 genomes]
rs34559117	0.81[ASN][1000 genomes]
rs3756247	0.81[ASN][1000 genomes]
rs3775956	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4301111	0.81[ASN][1000 genomes]
rs4396986	0.81[ASN][1000 genomes]
rs4484296	0.81[ASN][1000 genomes]
rs4549375	0.81[ASN][1000 genomes]
rs4554069	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449152	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815254	0.81[ASN][1000 genomes]
rs6815296	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816982	0.81[ASN][1000 genomes]
rs6827406	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839654	0.81[ASN][1000 genomes]
rs6843740	0.81[ASN][1000 genomes]
rs6848779	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7434484	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667175	0.81[ASN][1000 genomes]
rs7698596	0.81[ASN][1000 genomes]
rs9994518	0.90[AMR][1000 genomes];0.93[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	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
7	esv3361772	chr4:15666732-15684418	Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11722854	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 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	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach
4	chr4:15664800-15681800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:15668400-15682800	Weak transcription	Fetal Brain Male	brain
6	chr4:15668600-15681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:15669600-15681400	Weak transcription	Thymus	Thymus
8	chr4:15671000-15681600	Weak transcription	Fetal Lung	lung
9	chr4:15673800-15682800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:15675200-15682600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:15677400-15682800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr4:15677600-15682800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:15677800-15681000	Weak transcription	Primary B cells from cord blood	blood
14	chr4:15678600-15681200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:15678600-15681600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:15678800-15681400	Enhancers	Osteobl	bone
17	chr4:15679000-15681200	Enhancers	HepG2	liver
18	chr4:15679000-15681600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:15679000-15681800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:15679000-15682400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr4:15679200-15681600	Weak transcription	HSMM	muscle
22	chr4:15679200-15682200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:15679400-15681600	Weak transcription	Stomach Mucosa	stomach
24	chr4:15679400-15681800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:15679400-15682200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:15679400-15682800	Weak transcription	Pancreas	Pancrea
27	chr4:15679400-15685400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:15679400-15685600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:15679600-15681400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:15679600-15681400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr4:15679600-15681400	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr4:15679600-15681400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:15679600-15681600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:15679600-15681800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:15679600-15682000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:15679600-15682000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:15679600-15682600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:15679600-15682800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:15679600-15682800	Weak transcription	Esophagus	oesophagus
40	chr4:15679600-15684200	Active TSS	GM12878-XiMat	blood
41	chr4:15679600-15685400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr4:15679600-15685600	Active TSS	A549	lung
43	chr4:15680000-15681000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr4:15680000-15681200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:15680000-15681400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:15680000-15681800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:15680000-15682400	Flanking Active TSS	HUVEC	blood vessel
48	chr4:15680000-15682600	Weak transcription	Liver	Liver
49	chr4:15680200-15681200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:15680200-15681200	Active TSS	HMEC	breast

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