Variant report

Variant	rs4235379
Chromosome Location	chr4:15659278-15659279
allele	G/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:5)
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	MAFK	chr4:15659270-15659493	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
2	chr4:15649873..15653235-chr4:15657425..15660766,3	MCF-7	breast:
3	chr4:15469326..15470996-chr4:15657243..15660173,2	MCF-7	breast:
4	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:
5	chr4:15659126..15661222-chr4:15677719..15679356,2	MCF-7	breast:

No data

Variant related genes	Relation type
FBXL5	TF binding region
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10008376	0.96[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs10008975	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10214	0.96[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1125378	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs11728037	0.86[CHB][hapmap]
rs11728084	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12499412	0.92[EUR][1000 genomes]
rs12500587	0.90[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12500770	0.89[EUR][1000 genomes]
rs12512883	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12644655	0.86[EUR][1000 genomes]
rs12651550	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs13110674	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13120905	0.92[EUR][1000 genomes]
rs13129739	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13147590	0.93[EUR][1000 genomes]
rs1558572	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs1789	0.90[EUR][1000 genomes]
rs35414597	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270584	0.96[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs4358397	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4453929	0.87[EUR][1000 genomes]
rs4470622	0.88[EUR][1000 genomes]
rs4524378	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4557256	0.92[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs4616746	0.88[EUR][1000 genomes]
rs4631041	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4698402	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4698404	0.94[EUR][1000 genomes]
rs4698406	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698407	0.94[EUR][1000 genomes]
rs4698409	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs61021642	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6414765	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6414767	0.94[EUR][1000 genomes]
rs6449153	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6812708	0.80[CHD][hapmap]
rs6850169	0.85[EUR][1000 genomes]
rs6850422	0.96[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs7438356	0.96[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs7662032	0.94[EUR][1000 genomes]
rs7685083	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs7687003	0.89[EUR][1000 genomes]
rs7688984	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7690362	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7696127	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs7696938	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8180240	0.91[ASN][1000 genomes]
rs9918079	0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[YRI][hapmap]
rs9997068	0.92[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4235379	FBXL5	Cis_1M	lymphoblastoid	RTeQTL
rs4235379	FAM200B	cis	parietal	SCAN
rs4235379	CC2D2A	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15657200-15662200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr4:15657600-15681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:15657800-15659400	Weak transcription	Hela-S3	cervix
4	chr4:15657800-15659400	Weak transcription	HepG2	liver
5	chr4:15657800-15659600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:15657800-15659800	Weak transcription	A549	lung
7	chr4:15657800-15660000	Enhancers	NHDF-Ad	bronchial
8	chr4:15657800-15661400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:15657800-15666800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:15657800-15667800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:15658000-15659800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:15658000-15660600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr4:15658000-15661400	Weak transcription	Placenta	Placenta
14	chr4:15658000-15664600	Weak transcription	Esophagus	oesophagus
15	chr4:15658000-15665400	Weak transcription	Psoas Muscle	Psoas
16	chr4:15658000-15666800	Weak transcription	Thymus	Thymus
17	chr4:15658000-15667400	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:15658000-15667800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:15658000-15672200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:15658000-15673800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:15658200-15659400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:15658200-15659400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:15658200-15659400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:15658200-15659600	Enhancers	Osteobl	bone
28	chr4:15658200-15659800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:15658200-15660200	Enhancers	Fetal Lung	lung
30	chr4:15658200-15660400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:15658200-15661000	Weak transcription	Fetal Heart	heart
32	chr4:15658200-15661200	Weak transcription	Liver	Liver
33	chr4:15658200-15661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:15658200-15661800	Active TSS	Primary B cells from cord blood	blood
35	chr4:15658200-15665000	Weak transcription	GM12878-XiMat	blood
36	chr4:15658200-15666600	Weak transcription	HUVEC	blood vessel
37	chr4:15658200-15666800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:15658200-15667200	Weak transcription	Fetal Thymus	thymus
39	chr4:15658200-15667400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:15658200-15667400	Weak transcription	NH-A	brain
41	chr4:15658200-15667800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:15658200-15667800	Weak transcription	NHLF	lung
43	chr4:15658200-15668000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:15658200-15670600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:15658200-15679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:15658200-15679200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach
48	chr4:15658400-15659400	Weak transcription	Adipose Nuclei	Adipose
49	chr4:15658400-15659400	Weak transcription	HSMM	muscle
50	chr4:15658400-15659600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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