Variant report

Variant	rs762909
Chromosome Location	chr22:32930568-32930569
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	RAD21	chr22:32930340-32930802	HepG2	liver:	n/a	n/a
2	CEBPB	chr22:32930445-32930706	HepG2	liver:	n/a	n/a
3	MYC	chr22:32930516-32930714	HepG2	liver:	n/a	n/a
4	MYBL2	chr22:32930364-32930934	HepG2	liver:	n/a	n/a
5	RAD21	chr22:32930422-32930778	HepG2	liver:	n/a	n/a
6	RAD21	chr22:32930362-32930800	HepG2	liver:	n/a	n/a
7	CTCF	chr22:32930420-32930570	Caco-2	colon:	n/a	n/a
8	RFX5	chr22:32930532-32930712	HepG2	liver:	n/a	n/a
9	POLR2A	chr22:32929615-32930670	HepG2	liver:	n/a	n/a
10	MYBL2	chr22:32930311-32930922	HepG2	liver:	n/a	n/a
11	CEBPD	chr22:32930368-32930649	HepG2	liver:	n/a	n/a
12	HEY1	chr22:32929756-32930731	HepG2	liver:	n/a	n/a
13	POLR2A	chr22:32929685-32930738	HepG2	liver:	n/a	n/a
14	ZBTB7A	chr22:32930287-32930615	HepG2	liver:	n/a	n/a
15	FOXA2	chr22:32930387-32930788	HepG2	liver:	n/a	n/a
16	NR3C1	chr22:32930455-32930793	A549	lung:	n/a	n/a
17	YY1	chr22:32930149-32930724	HepG2	liver:	n/a	n/a
18	CEBPB	chr22:32930401-32930731	HepG2	liver:	n/a	n/a
19	CEBPB	chr22:32930426-32930588	HepG2	liver:	n/a	n/a
20	POLR2A	chr22:32929876-32930702	HepG2	liver:	n/a	n/a
21	ZBTB7A	chr22:32930306-32930608	HepG2	liver:	n/a	n/a
22	HNF4A	chr22:32930422-32930801	HepG2	liver:	n/a	chr22:32930560-32930575 chr22:32930562-32930574 chr22:32930562-32930574 chr22:32930562-32930574 chr22:32930562-32930575 chr22:32930561-32930574 chr22:32930560-32930575 chr22:32930560-32930575 chr22:32930560-32930575 chr22:32930562-32930575
23	EP300	chr22:32930292-32930906	HepG2	liver:	n/a	n/a
24	HNF4G	chr22:32930349-32930816	HepG2	liver:	n/a	chr22:32930560-32930575 chr22:32930561-32930576 chr22:32930388-32930402 chr22:32930562-32930574 chr22:32930562-32930574 chr22:32930562-32930574 chr22:32930562-32930575 chr22:32930561-32930574 chr22:32930560-32930575 chr22:32930560-32930575 chr22:32930562-32930575
25	NFIC	chr22:32930446-32930735	HepG2	liver:	n/a	n/a
26	CHD2	chr22:32930193-32930817	HepG2	liver:	n/a	n/a
27	HDAC2	chr22:32930292-32930808	HepG2	liver:	n/a	n/a
28	HNF4A	chr22:32930346-32930736	HepG2	liver:	n/a	chr22:32930560-32930575 chr22:32930388-32930402 chr22:32930562-32930574 chr22:32930562-32930574 chr22:32930562-32930574 chr22:32930562-32930575 chr22:32930561-32930574 chr22:32930560-32930575 chr22:32930560-32930575 chr22:32930560-32930575 chr22:32930562-32930575
29	POLR2A	chr22:32930436-32930783	HepG2	liver:	n/a	n/a
30	TBP	chr22:32930375-32930712	HepG2	liver:	n/a	n/a
31	MAZ	chr22:32930267-32930793	HepG2	liver:	n/a	n/a
32	SP1	chr22:32930379-32930817	HepG2	liver:	n/a	n/a
33	NR3C1	chr22:32930425-32930876	A549	lung:	n/a	n/a
34	CTCF	chr22:32930480-32930630	Caco-2	colon:	n/a	chr22:32930577-32930590
35	SMC3	chr22:32930497-32930740	HepG2	liver:	n/a	n/a
36	EP300	chr22:32930489-32930880	HepG2	liver:	n/a	n/a
37	NR3C1	chr22:32930450-32930710	A549	lung:	n/a	n/a
38	HEY1	chr22:32930126-32930670	HepG2	liver:	n/a	n/a
39	POLR2A	chr22:32930388-32930653	HepG2	liver:	n/a	n/a
40	CTCF	chr22:32930520-32930670	NHDF-neo	bronchial:	n/a	chr22:32930577-32930590
41	POLR2A	chr22:32930364-32930750	HepG2	liver:	n/a	n/a
42	CTCF	chr22:32930460-32930610	HepG2	liver:	n/a	chr22:32930577-32930590

No.	Distal block	Cell Line	Cell type
1	chr22:32927409..32931156-chr22:32954969..32961432,7	MCF-7	breast:
2	chr22:32930315..32931946-chr22:32951753..32954343,3	MCF-7	breast:
3	chr22:32928149..32930709-chr22:33046752..33049031,2	MCF-7	breast:
4	chr22:32928103..32930722-chr22:32934980..32936586,2	MCF-7	breast:
5	chr22:32930459..32932142-chr22:32971211..32972775,2	MCF-7	breast:
6	chr22:32928792..32930842-chr22:32975300..32976843,2	MCF-7	breast:

Variant related genes	Relation type
SYN3	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs135123	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs135474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs135476	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs135478	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs135480	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs135483	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2105865	0.88[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs2213405	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2251400	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710380	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs2858339	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749457	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754137	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs5754138	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs5754139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs762908	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9609593	0.94[ASN][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	nsv914981	chr22:32912277-32940660	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32914400-32932000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:32923600-32931400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr22:32924200-32932200	Enhancers	Placenta	Placenta
4	chr22:32924600-32932000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr22:32924600-32932800	Enhancers	Fetal Muscle Leg	muscle
6	chr22:32924800-32931000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr22:32924800-32931200	Enhancers	Fetal Lung	lung
8	chr22:32924800-32931200	Enhancers	NHDF-Ad	bronchial
9	chr22:32924800-32932200	Enhancers	Fetal Stomach	stomach
10	chr22:32925200-32931000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr22:32925600-32930600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr22:32926800-32930800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr22:32926800-32932200	Enhancers	Left Ventricle	heart
14	chr22:32927000-32931000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr22:32927200-32930800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:32927200-32931000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr22:32927200-32931000	Enhancers	Osteobl	bone
18	chr22:32927400-32931000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr22:32927600-32931800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:32927800-32932200	Enhancers	Right Ventricle	heart
21	chr22:32928000-32930800	Enhancers	Colonic Mucosa	Colon
22	chr22:32928000-32930800	Enhancers	Lung	lung
23	chr22:32928000-32930800	Enhancers	NH-A	brain
24	chr22:32928000-32931000	Enhancers	Pancreas	Pancrea
25	chr22:32928000-32931200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr22:32928000-32932200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr22:32928400-32934400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr22:32928400-32935800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr22:32928400-32935800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr22:32928400-32937600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr22:32928600-32931200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr22:32928600-32931400	Enhancers	NHLF	lung
33	chr22:32928600-32931600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr22:32928600-32931600	Enhancers	Fetal Muscle Trunk	muscle
35	chr22:32928600-32931800	Enhancers	Adipose Nuclei	Adipose
36	chr22:32928600-32935600	Weak transcription	Fetal Intestine Large	intestine
37	chr22:32929000-32930600	Weak transcription	Gastric	stomach
38	chr22:32929000-32931400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr22:32929000-32940800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr22:32929200-32930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr22:32929200-32931200	Enhancers	HSMMtube	muscle
42	chr22:32929200-32931600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr22:32929200-32931800	Enhancers	Hela-S3	cervix
44	chr22:32929400-32931000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr22:32929400-32932000	Weak transcription	Esophagus	oesophagus
46	chr22:32929600-32930800	Enhancers	Brain Substantia Nigra	brain
47	chr22:32929600-32931000	Enhancers	Liver	Liver
48	chr22:32929600-32931000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr22:32929600-32931200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr22:32929800-32930800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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