Variant report

Variant	rs1440742
Chromosome Location	chr4:68752092-68752093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr4:68751247-68752482	SK-N-SH	brain:	n/a	n/a
2	RCOR1	chr4:68751231-68752396	IMR90	lung:	n/a	n/a
3	EP300	chr4:68751991-68752315	SK-N-SH_RA	brain:	n/a	chr4:68752174-68752183
4	TCF12	chr4:68751380-68752536	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr4:68750509-68753035	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr4:68751281-68752523	HUVEC	blood vessel:	n/a	chr4:68751673-68751685
7	POLR2A	chr4:68751912-68752130	Hela-S3	cervix:	n/a	n/a
8	MAFK	chr4:68751396-68752547	IMR90	lung:	n/a	n/a
9	STAT3	chr4:68751258-68752660	MCF10A-Er-Src	breast:	n/a	chr4:68751507-68751516 chr4:68751504-68751518 chr4:68752184-68752193 chr4:68751506-68751515
10	CHD1	chr4:68751078-68752771	IMR90	lung:	n/a	n/a
11	FOS	chr4:68751359-68752606	MCF10A-Er-Src	breast:	n/a	chr4:68751673-68751685
12	STAT3	chr4:68751093-68752965	MCF10A-Er-Src	breast:	n/a	chr4:68751507-68751516 chr4:68751504-68751518 chr4:68752850-68752873 chr4:68752184-68752193 chr4:68751506-68751515
13	JUND	chr4:68751330-68752553	SK-N-SH	brain:	n/a	chr4:68751673-68751685
14	FOS	chr4:68752066-68752392	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr4:68751345-68752725	MCF10A-Er-Src	breast:	n/a	chr4:68751673-68751685
16	EP300	chr4:68751322-68752412	SK-N-SH	brain:	n/a	chr4:68752174-68752183 chr4:68751812-68751825
17	MAX	chr4:68751566-68752338	NB4	blood:	n/a	n/a
18	CEBPB	chr4:68751495-68752334	IMR90	lung:	n/a	chr4:68752041-68752054
19	POLR2A	chr4:68751863-68752325	HUVEC	blood vessel:	n/a	n/a
20	FOS	chr4:68751297-68752630	MCF10A-Er-Src	breast:	n/a	chr4:68751673-68751685
21	POLR2A	chr4:68751974-68752243	Hela-S3	cervix:	n/a	n/a
22	JUN	chr4:68751456-68752380	HUVEC	blood vessel:	n/a	chr4:68751673-68751685
23	MYC	chr4:68752083-68752416	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr4:68751423-68752443	HUVEC	blood vessel:	n/a	n/a
25	JUND	chr4:68751327-68752452	SK-N-SH	brain:	n/a	chr4:68751673-68751685
26	FOSL2	chr4:68751410-68752484	SK-N-SH	brain:	n/a	chr4:68751673-68751685
27	JUND	chr4:68751351-68752485	SK-N-SH	brain:	n/a	chr4:68751673-68751685
28	STAT3	chr4:68751105-68752679	MCF10A-Er-Src	breast:	n/a	chr4:68751507-68751516 chr4:68751504-68751518 chr4:68752184-68752193 chr4:68751506-68751515
29	POLR2A	chr4:68751391-68752333	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:68747971..68750609-chr4:68750969..68752547,2	MCF-7	breast:

Variant related genes	Relation type
TMPRSS11D	TF binding region
ENSG00000153802	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12642332	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371934	0.81[CEU][hapmap]
rs1371935	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1438426	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1438427	0.98[ASN][1000 genomes]
rs1440740	0.81[CEU][hapmap]
rs1440741	0.81[CEU][hapmap]
rs1440743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595934	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1899219	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2053441	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2119382	0.98[ASN][1000 genomes]
rs2119383	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2874062	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35187434	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353152	0.82[EUR][1000 genomes]
rs353156	0.96[ASN][1000 genomes]
rs353159	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs353161	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353163	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353170	0.99[ASN][1000 genomes]
rs353173	0.99[ASN][1000 genomes]
rs353174	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4860264	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4860862	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4860864	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6842660	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959636	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9992096	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879214	chr4:68389841-68789778	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv829960	chr4:68649237-68809629	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1007376	chr4:68693483-69008202	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1811886	chr4:68725776-68780041	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv879219	chr4:68743032-69028913	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:68741400-68752800	Weak transcription	Esophagus	oesophagus
2	chr4:68744800-68752800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr4:68750000-68752600	Enhancers	NHDF-Ad	bronchial
4	chr4:68750200-68752600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:68750800-68752400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:68751200-68752200	Flanking Active TSS	HUVEC	blood vessel
7	chr4:68751200-68752400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:68751200-68752400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr4:68751400-68752200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr4:68751400-68752400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr4:68751400-68752800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:68751400-68753000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:68751400-68753000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:68751400-68753000	Enhancers	HMEC	breast
15	chr4:68751400-68753200	Enhancers	HSMM	muscle
16	chr4:68751600-68752400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr4:68751600-68752600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:68751600-68752600	Enhancers	Primary hematopoietic stem cells	blood
19	chr4:68751600-68752800	Enhancers	NHLF	lung
20	chr4:68751800-68752200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:68751800-68752200	Flanking Active TSS	NH-A	brain
22	chr4:68751800-68752200	Flanking Active TSS	NHEK	skin
23	chr4:68751800-68752400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:68751800-68752400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:68751800-68752400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr4:68751800-68752400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:68751800-68752400	Enhancers	Osteobl	bone
28	chr4:68751800-68753200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:68751800-68753200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:68752000-68752200	Flanking Active TSS	Hela-S3	cervix
31	chr4:68752000-68752400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:68752000-68752400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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