Variant report

Variant	rs6048544
Chromosome Location	chr20:23071031-23071032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:23070881-23071187	K562	blood:	n/a	n/a
2	CTCF	chr20:23070860-23071153	K562	blood:	n/a	n/a
3	CTCF	chr20:23070940-23071090	Caco-2	colon:	n/a	n/a
4	RAD21	chr20:23070705-23071261	HCT-116	colon:	n/a	chr20:23070927-23070940
5	CTCF	chr20:23070928-23071120	K562	blood:	n/a	n/a
6	CTCF	chr20:23070975-23071044	MCF-7	breast:	n/a	n/a
7	CTCF	chr20:23070980-23071130	HCT-116	colon:	n/a	n/a
8	CTCF	chr20:23070977-23071078	GM12878	blood:	n/a	n/a
9	CTCF	chr20:23070986-23071046	GM12891	blood:	n/a	n/a
10	CTCF	chr20:23070920-23071112	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAZ	chr20:23070870-23071096	K562	blood:	n/a	n/a
12	RAD21	chr20:23070893-23071136	H1-hESC	embryonic stem cell:	n/a	chr20:23070927-23070940
13	CTCF	chr20:23070833-23071202	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr20:23070960-23071110	GM12874	blood:	n/a	n/a
15	CTCF	chr20:23070859-23071232	K562	blood:	n/a	n/a
16	CTCF	chr20:23070960-23071110	HepG2	liver:	n/a	n/a
17	CTCF	chr20:23070960-23071110	GM12870	blood:	n/a	n/a
18	CTCF	chr20:23070960-23071110	GM06990	blood:	n/a	n/a
19	CTCF	chr20:23070935-23071074	MCF-7	breast:	n/a	n/a
20	CTCF	chr20:23070980-23071035	MCF-7	breast:	n/a	n/a
21	CTCF	chr20:23070900-23071050	HEK293	kidney:	n/a	n/a
22	CTCF	chr20:23070900-23071050	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr20:23070975-23071055	GM12892	blood:	n/a	n/a
24	CTCF	chr20:23070960-23071110	K562	blood:	n/a	n/a
25	CTCF	chr20:23070960-23071043	HepG2	liver:	n/a	n/a
26	RAD21	chr20:23070755-23071161	H1-hESC	embryonic stem cell:	n/a	chr20:23070927-23070940
27	CTCF	chr20:23071005-23071035	A549	lung:	n/a	n/a
28	CTCF	chr20:23070794-23071159	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr20:23070726-23071292	HCT-116	colon:	n/a	n/a
30	CTCF	chr20:23070920-23071070	GM12869	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23069239..23071325-chr20:23078178..23079925,2	K562	blood:
2	chr20:23070657..23074611-chr20:23139526..23144408,4	K562	blood:
3	chr20:23068190..23071729-chr20:23127032..23130141,4	K562	blood:
4	chr20:23063544..23069652-chr20:23069895..23074755,10	K562	blood:
5	chr20:23070987..23074715-chr20:23112780..23116931,4	K562	blood:
6	chr20:23063060..23067662-chr20:23069728..23074122,5	K562	blood:

No data

Variant related genes	Relation type
CD93	TF binding region
ENSG00000201527	Chromatin interaction
ENSG00000125810	Chromatin interaction
ENSG00000233746	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1856471	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048545	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048546	1.00[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62202612	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs844814	0.82[EUR][1000 genomes]
rs844819	0.81[EUR][1000 genomes]
rs844821	0.81[EUR][1000 genomes]
rs844822	0.81[EUR][1000 genomes]
rs844825	0.81[EUR][1000 genomes]
rs844827	0.81[EUR][1000 genomes]
rs844831	0.80[EUR][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	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv526474	chr20:23065209-23073904	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6048544	FOXO3	trans	parietal	SCAN
rs6048544	THBD	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23064000-23072000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23064200-23072000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr20:23064200-23072400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr20:23066000-23075800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:23067000-23072000	Weak transcription	Pancreas	Pancrea
6	chr20:23067000-23073800	Weak transcription	Esophagus	oesophagus
7	chr20:23067200-23071400	Weak transcription	Ovary	ovary
8	chr20:23067200-23072200	Weak transcription	Lung	lung
9	chr20:23067400-23072400	Weak transcription	Fetal Lung	lung
10	chr20:23067800-23072400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr20:23068400-23072400	Weak transcription	Left Ventricle	heart
12	chr20:23068400-23072400	Weak transcription	Right Atrium	heart
13	chr20:23068400-23072400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr20:23068600-23073600	Weak transcription	Spleen	Spleen
15	chr20:23068800-23072600	Weak transcription	Adipose Nuclei	Adipose
16	chr20:23068800-23072800	Enhancers	K562	blood
17	chr20:23069000-23072400	Weak transcription	Placenta	Placenta
18	chr20:23069000-23080400	Weak transcription	Fetal Thymus	thymus
19	chr20:23069200-23072200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr20:23069600-23071400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr20:23069600-23071800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr20:23069600-23072000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr20:23069800-23072000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr20:23070200-23071400	Bivalent Enhancer	Fetal Stomach	stomach
25	chr20:23070800-23072000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr20:23070800-23074400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr20:23071000-23071200	Enhancers	Fetal Muscle Leg	muscle
28	chr20:23071000-23072000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr20:23071000-23072400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr20:23071000-23074400	Enhancers	HUVEC	blood vessel

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