Variant report

Variant	rs1404301
Chromosome Location	chr5:119949505-119949506
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	CTCF	chr5:119949500-119949650	HMF	breast:	n/a	n/a
2	CTCF	chr5:119949440-119949590	NHDF-neo	bronchial:	n/a	n/a
3	CTCF	chr5:119949500-119949650	AG04450	lung:	n/a	n/a
4	CTCF	chr5:119949400-119949550	HMEC	breast:	n/a	n/a
5	CTCF	chr5:119949480-119949630	AG09319	gingival:	n/a	n/a
6	CTCF	chr5:119949380-119949530	HFF	foreskin:	n/a	n/a
7	CTCF	chr5:119949480-119949630	AG04450	lung:	n/a	n/a
8	CTCF	chr5:119949440-119949590	AG10803	skin:	n/a	n/a
9	FOS	chr5:119949388-119949781	MCF10A-Er-Src	breast:	n/a	chr5:119949438-119949450
10	CTCF	chr5:119949440-119949590	HMF	breast:	n/a	n/a
11	CTCF	chr5:119949460-119949610	RPTEC	kidney:	n/a	n/a
12	CTCF	chr5:119949400-119949550	RPTEC	kidney:	n/a	n/a
13	CTCF	chr5:119949460-119949610	HCPEpiC	choroid plexus:	n/a	n/a
14	FOS	chr5:119949450-119949739	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr5:119949400-119949550	HPF	lung:	n/a	n/a

Variant related genes	Relation type
PRR16	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1584466	0.82[AFR][1000 genomes]
rs1584467	0.82[AFR][1000 genomes]
rs1997003	0.82[AFR][1000 genomes]
rs2018396	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2085178	1.00[AMR][1000 genomes]
rs6595244	1.00[AMR][1000 genomes]
rs73256047	1.00[AMR][1000 genomes]
rs73256058	1.00[AMR][1000 genomes]
rs73256063	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830463	chr5:119806643-119968825	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv948613	chr5:119861955-119999008	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv599602	chr5:119866504-120023393	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv949499	chr5:119869763-119999008	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119938800-119950000	Weak transcription	Aorta	Aorta
2	chr5:119941800-119950200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr5:119942600-119949600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:119942600-119952800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:119945800-119949800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:119946400-119949800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:119948200-119952000	Enhancers	Osteobl	bone
8	chr5:119948400-119949800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr5:119948600-119949600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:119948600-119949600	Enhancers	NHDF-Ad	bronchial
11	chr5:119948600-119950400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:119948600-119952000	Enhancers	HSMM	muscle
13	chr5:119948800-119950000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:119949200-119950400	Enhancers	NH-A	brain
15	chr5:119949200-119953000	Enhancers	NHLF	lung
16	chr5:119949400-119949600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:119949400-119949600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:119949400-119950000	Enhancers	HSMMtube	muscle
19	chr5:119949400-119950200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:119949400-119950600	Enhancers	Brain Cingulate Gyrus	brain
21	chr5:119949400-119951000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:119949400-119951800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:119949400-119952400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:119949400-119953000	Enhancers	HMEC	breast
25	chr5:119949400-119953000	Enhancers	NHEK	skin

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