Variant report

Variant	rs6850169
Chromosome Location	chr4:15682252-15682253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:15682122-15682389	Hela-S3	cervix:	n/a	n/a
2	TCF7L2	chr4:15682123-15682323	Hela-S3	cervix:	n/a	n/a
3	CHD1	chr4:15682231-15684731	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr4:15682135-15682383	HepG2	liver:	n/a	n/a
5	CEBPB	chr4:15682164-15682389	H1-hESC	embryonic stem cell:	n/a	n/a
6	GTF3C2	chr4:15681943-15682401	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr4:15681982-15682319	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr4:15682215-15682306	K562	blood:	n/a	n/a
9	GTF3C2	chr4:15681935-15682390	K562	blood:	n/a	n/a
10	TBL1XR1	chr4:15681444-15682382	K562	blood:	n/a	n/a
11	ZNF384	chr4:15681972-15682422	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:15681714..15684664-chr4:16226494..16229781,3	K562	blood:
2	chr4:15681636..15683511-chr4:15686226..15688652,2	K562	blood:
3	chr4:15681678..15685124-chr4:15685309..15687808,5	MCF-7	breast:
4	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
5	chr4:15652080..15658606-chr4:15677363..15685579,17	MCF-7	breast:
6	chr4:15655595..15658742-chr4:15680185..15687360,10	MCF-7	breast:
7	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:

No data

Variant related genes	Relation type
FAM200B	TF binding region
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction
ENSG00000169762	Chromatin interaction
ENSG00000263327	Chromatin interaction

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

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

rs_ID	r²[population]
rs10008376	0.84[EUR][1000 genomes]
rs10008975	0.83[EUR][1000 genomes]
rs10214	0.82[EUR][1000 genomes]
rs11728084	0.82[EUR][1000 genomes]
rs12499412	0.83[EUR][1000 genomes]
rs12500587	0.81[EUR][1000 genomes]
rs12500770	0.81[EUR][1000 genomes]
rs12644655	0.84[EUR][1000 genomes]
rs12651550	0.85[EUR][1000 genomes]
rs13110674	0.84[EUR][1000 genomes]
rs13120905	0.83[EUR][1000 genomes]
rs13147590	0.84[EUR][1000 genomes]
rs1789	0.86[EUR][1000 genomes]
rs4235379	0.85[EUR][1000 genomes]
rs4358397	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4453929	0.90[EUR][1000 genomes]
rs4470622	0.91[EUR][1000 genomes]
rs4524378	0.83[EUR][1000 genomes]
rs4557256	0.83[EUR][1000 genomes]
rs4616746	0.91[EUR][1000 genomes]
rs4631041	0.90[EUR][1000 genomes]
rs4698402	0.85[EUR][1000 genomes]
rs4698404	0.85[EUR][1000 genomes]
rs4698406	0.85[EUR][1000 genomes]
rs4698407	0.85[EUR][1000 genomes]
rs4698409	0.89[EUR][1000 genomes]
rs61021642	0.81[EUR][1000 genomes]
rs6414765	0.84[EUR][1000 genomes]
rs6414767	0.85[EUR][1000 genomes]
rs6449153	0.88[EUR][1000 genomes]
rs6850422	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7438356	0.84[EUR][1000 genomes]
rs7662032	0.85[EUR][1000 genomes]
rs7685083	0.83[EUR][1000 genomes]
rs7687003	0.87[EUR][1000 genomes]
rs7688984	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7690362	0.85[ASN][1000 genomes]
rs7696127	0.84[EUR][1000 genomes]
rs7696938	0.85[ASN][1000 genomes]
rs8180240	0.87[ASN][1000 genomes]
rs9997068	0.83[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	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
rs6850169	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15668400-15682800	Weak transcription	Fetal Brain Male	brain
2	chr4:15673800-15682800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:15675200-15682600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:15677400-15682800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:15677600-15682800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:15679000-15682400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr4:15679400-15682800	Weak transcription	Pancreas	Pancrea
8	chr4:15679400-15685400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:15679400-15685600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:15679600-15682600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:15679600-15682800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:15679600-15682800	Weak transcription	Esophagus	oesophagus
13	chr4:15679600-15684200	Active TSS	GM12878-XiMat	blood
14	chr4:15679600-15685400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:15679600-15685600	Active TSS	A549	lung
16	chr4:15680000-15682400	Flanking Active TSS	HUVEC	blood vessel
17	chr4:15680000-15682600	Weak transcription	Liver	Liver
18	chr4:15680200-15685000	Active TSS	K562	blood
19	chr4:15680400-15682400	Flanking Active TSS	Dnd41	blood
20	chr4:15680400-15684200	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr4:15680800-15684800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:15681000-15685400	Active TSS	NH-A	brain
23	chr4:15681200-15684200	Active TSS	NHDF-Ad	bronchial
24	chr4:15681400-15682400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr4:15681400-15682600	Enhancers	Fetal Intestine Large	intestine
26	chr4:15681400-15683200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr4:15681400-15683200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:15681400-15683400	Active TSS	Brain Germinal Matrix	brain
29	chr4:15681400-15684400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:15681400-15684600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr4:15681400-15684600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:15681400-15684800	Active TSS	Thymus	Thymus
33	chr4:15681600-15682600	Enhancers	Primary B cells from cord blood	blood
34	chr4:15681600-15682600	Enhancers	Primary hematopoietic stem cells	blood
35	chr4:15681600-15682600	Enhancers	Fetal Lung	lung
36	chr4:15681600-15684400	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr4:15681600-15684600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:15681600-15684600	Active TSS	HSMM	muscle
39	chr4:15681600-15684800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:15681600-15684800	Active TSS	Fetal Thymus	thymus
41	chr4:15681600-15685400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:15681800-15682400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr4:15681800-15682600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr4:15681800-15683200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:15681800-15683800	Active TSS	Hela-S3	cervix
46	chr4:15681800-15684000	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr4:15681800-15684400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr4:15681800-15684600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:15681800-15684600	Active TSS	NHEK	skin
50	chr4:15681800-15685600	Active TSS	NHLF	lung

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