Variant report

Variant	rs6564744
Chromosome Location	chr16:80208157-80208158
allele	A/G
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	CEBPB	chr16:80208154-80208835	A549	lung:	n/a	chr16:80208521-80208532 chr16:80208519-80208532 chr16:80208519-80208532 chr16:80208519-80208530 chr16:80208521-80208532
2	MAX	chr16:80208142-80208792	A549	lung:	n/a	n/a
3	SP1	chr16:80208106-80208695	A549	lung:	n/a	n/a
4	POLR2A	chr16:80208152-80208676	U87	brain:	n/a	n/a
5	EP300	chr16:80208137-80208812	A549	lung:	n/a	chr16:80208520-80208534
6	USF1	chr16:80208138-80208662	A549	lung:	n/a	n/a
7	GATA3	chr16:80208062-80208785	A549	lung:	n/a	n/a
8	TCF12	chr16:80208101-80208835	A549	lung:	n/a	n/a
9	FOS	chr16:80208078-80208681	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:80204436..80206073-chr16:80206185..80208227,2	MCF-7	breast:
2	chr16:80208061..80210016-chr16:80210525..80213135,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261376	TF binding region
ENSG00000261376	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11640831	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11643917	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12716882	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1382389	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs16944269	0.80[EUR][1000 genomes]
rs1871209	0.88[AFR][1000 genomes]
rs1904186	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2169804	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2169806	1.00[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4889112	0.84[AFR][1000 genomes]
rs4889115	0.80[AFR][1000 genomes]
rs4889116	0.88[ASN][1000 genomes]
rs62049508	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7186149	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7189918	0.90[AFR][1000 genomes]
rs7201276	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7205467	0.84[AFR][1000 genomes]
rs8045952	0.84[AFR][1000 genomes]
rs8047391	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8061813	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9673185	0.88[AFR][1000 genomes]
rs9930130	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9935652	0.91[ASN][1000 genomes]
rs9939067	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9940589	0.89[ASN][1000 genomes]
rs9944373	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833298	chr16:80122337-80314603	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1055228	chr16:80207546-80378842	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1061068	chr16:80207546-80537052	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6564744	CFDP1	cis	parietal	SCAN
rs6564744	C16orf46	cis	cerebellum	SCAN
rs6564744	VAT1L	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80206600-80208400	Enhancers	Placenta	Placenta
2	chr16:80207400-80210600	Enhancers	NHDF-Ad	bronchial
3	chr16:80207600-80210000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:80207600-80210600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr16:80207600-80212200	Enhancers	Osteobl	bone
6	chr16:80207800-80208400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr16:80207800-80208600	Enhancers	NHLF	lung
8	chr16:80207800-80208800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr16:80207800-80210000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:80207800-80210000	Enhancers	HSMM	muscle
11	chr16:80207800-80210200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr16:80207800-80210200	Enhancers	HUVEC	blood vessel
13	chr16:80207800-80210200	Enhancers	NH-A	brain
14	chr16:80207800-80210400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr16:80207800-80210400	Enhancers	HMEC	breast
16	chr16:80207800-80210400	Enhancers	HSMMtube	muscle
17	chr16:80207800-80210400	Enhancers	NHEK	skin
18	chr16:80207800-80210800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr16:80207800-80212200	Enhancers	A549	lung
20	chr16:80208000-80208200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr16:80208000-80208400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr16:80208000-80209200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:80208000-80209600	Enhancers	Hela-S3	cervix
24	chr16:80208000-80210200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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