Variant report

Variant	rs73904107
Chromosome Location	chr20:22547939-22547940
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr20:22547811-22548264	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr20:22547089-22548440	H1-neurons	neurons:	n/a	n/a
3	SUZ12	chr20:22547785-22550361	NT2-D1	testis:	n/a	n/a
4	MAX	chr20:22547839-22548148	H1-hESC	embryonic stem cell:	n/a	n/a
5	USF1	chr20:22547823-22548212	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr20:22547566-22548500	HepG2	liver:	n/a	n/a
7	POLR2A	chr20:22547669-22548200	H1-neurons	neurons:	n/a	n/a
8	STAT3	chr20:22547914-22548061	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:22537625..22541473-chr20:22546828..22550085,4	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXA2-2	chr20:22547934-22547993	XLOC_013684
2	lnc-FOXA2-2	chr20:22547321-22548523	NONHSAT078988

No data

Variant related genes	Relation type
LINC00261	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1157319	1.00[AMR][1000 genomes]
rs12624528	1.00[AMR][1000 genomes]
rs1415812	1.00[AMR][1000 genomes]
rs16984026	1.00[AMR][1000 genomes]
rs16984047	1.00[AMR][1000 genomes]
rs1933205	1.00[AMR][1000 genomes]
rs3920804	1.00[AMR][1000 genomes]
rs55643169	1.00[AMR][1000 genomes]
rs55663904	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55789916	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55848868	1.00[AMR][1000 genomes]
rs58225430	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60516763	1.00[AMR][1000 genomes]
rs6106535	1.00[AMR][1000 genomes]
rs61590736	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72470560	1.00[AMR][1000 genomes]
rs7270376	1.00[AMR][1000 genomes]
rs7270463	1.00[AMR][1000 genomes]
rs73900505	1.00[AMR][1000 genomes]
rs73900511	1.00[AMR][1000 genomes]
rs73900515	1.00[AMR][1000 genomes]
rs73900516	1.00[AMR][1000 genomes]
rs73900531	1.00[AMR][1000 genomes]
rs73900532	1.00[AMR][1000 genomes]
rs73900535	1.00[AMR][1000 genomes]
rs73902812	1.00[AMR][1000 genomes]
rs73902816	1.00[AMR][1000 genomes]
rs73902820	1.00[AMR][1000 genomes]
rs73902823	1.00[AMR][1000 genomes]
rs73902824	1.00[AMR][1000 genomes]
rs73902838	1.00[AMR][1000 genomes]
rs73902839	1.00[AMR][1000 genomes]
rs73902840	1.00[AMR][1000 genomes]
rs73902841	1.00[AMR][1000 genomes]
rs73902843	1.00[AMR][1000 genomes]
rs73902845	1.00[AMR][1000 genomes]
rs73902848	1.00[AMR][1000 genomes]
rs73902849	1.00[AMR][1000 genomes]
rs73902851	1.00[AMR][1000 genomes]
rs73902855	1.00[AMR][1000 genomes]
rs73902857	1.00[AMR][1000 genomes]
rs73902859	1.00[AMR][1000 genomes]
rs73902863	1.00[AMR][1000 genomes]
rs73902864	1.00[AMR][1000 genomes]
rs73902865	1.00[AMR][1000 genomes]
rs73902866	1.00[AMR][1000 genomes]
rs73902868	1.00[AMR][1000 genomes]
rs73902874	1.00[AMR][1000 genomes]
rs73902880	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902891	0.91[AFR][1000 genomes]
rs73902892	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902897	0.91[AFR][1000 genomes]
rs73902898	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902900	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902901	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902902	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904103	0.95[AFR][1000 genomes]
rs73904105	0.95[AFR][1000 genomes]
rs8118829	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428690	chr20:22528757-22649625	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22540000-22548800	Weak transcription	Gastric	stomach
2	chr20:22543200-22548000	Weak transcription	K562	blood
3	chr20:22544400-22548000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr20:22544600-22549400	Genic enhancers	Liver	Liver
5	chr20:22545600-22548600	Weak transcription	Pancreas	Pancrea
6	chr20:22546600-22548000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr20:22546600-22548800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
8	chr20:22547000-22548200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr20:22547000-22548400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
10	chr20:22547000-22550800	Strong transcription	HepG2	liver
11	chr20:22547200-22548000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
12	chr20:22547200-22548200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
13	chr20:22547200-22549000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr20:22547800-22548000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
15	chr20:22547800-22548000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
16	chr20:22547800-22548000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
17	chr20:22547800-22548000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
18	chr20:22547800-22548000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr20:22547800-22548000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
20	chr20:22547800-22548000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
21	chr20:22547800-22549800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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