Variant report

Variant	rs9620817
Chromosome Location	chr22:29108556-29108557
allele	A/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	NFIC	chr22:29107956-29108677	HepG2	liver:	n/a	n/a
2	ARID3A	chr22:29107841-29108771	HepG2	liver:	n/a	n/a
3	GATA3	chr22:29108140-29109012	SK-N-SH	brain:	n/a	n/a
4	FOXA2	chr22:29107917-29108663	HepG2	liver:	n/a	n/a
5	MAX	chr22:29107979-29108753	Hela-S3	cervix:	n/a	n/a
6	JUN	chr22:29107986-29108802	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr22:29108404-29108597	K562	blood:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539
8	SP1	chr22:29107981-29108817	A549	lung:	n/a	n/a
9	MYC	chr22:29108378-29108719	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr22:29107903-29108935	A549	lung:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539 chr22:29108258-29108269
11	RFX5	chr22:29107894-29108846	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr22:29108408-29108696	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr22:29108293-29108780	ECC-1	luminal epithelium:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539
14	STAT3	chr22:29108246-29108732	MCF10A-Er-Src	breast:	n/a	chr22:29108269-29108292 chr22:29108269-29108277 chr22:29108530-29108538
15	PBX3	chr22:29108162-29108829	SK-N-SH	brain:	n/a	n/a
16	EP300	chr22:29107489-29108826	Hela-S3	cervix:	n/a	chr22:29107640-29107654 chr22:29108372-29108382
17	EP300	chr22:29108370-29108694	SK-N-SH_RA	brain:	n/a	chr22:29108372-29108382
18	TCF12	chr22:29108253-29108764	A549	lung:	n/a	n/a
19	POLR2A	chr22:29108453-29108729	MCF10A-Er-Src	breast:	n/a	n/a
20	EP300	chr22:29107943-29108686	HepG2	liver:	n/a	chr22:29108372-29108382
21	TCF7L2	chr22:29108156-29108713	Hela-S3	cervix:	n/a	chr22:29108453-29108460 chr22:29108450-29108460
22	MBD4	chr22:29108097-29108702	HepG2	liver:	n/a	n/a
23	TCF7L2	chr22:29108288-29108608	HepG2	liver:	n/a	chr22:29108453-29108460 chr22:29108450-29108460
24	ZBTB33	chr22:29108380-29108721	A549	lung:	n/a	n/a
25	STAT3	chr22:29107909-29108815	Hela-S3	cervix:	n/a	chr22:29108269-29108292 chr22:29108269-29108277 chr22:29108530-29108538
26	FOXA2	chr22:29108068-29108657	A549	lung:	n/a	n/a
27	EP300	chr22:29108303-29108768	SK-N-SH_RA	brain:	n/a	chr22:29108372-29108382
28	CEBPB	chr22:29108402-29108673	HepG2	liver:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539
29	FOS	chr22:29108365-29108794	MCF10A-Er-Src	breast:	n/a	n/a
30	CEBPB	chr22:29108294-29108738	ECC-1	luminal epithelium:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539
31	JUND	chr22:29107938-29108776	Hela-S3	cervix:	n/a	n/a
32	EP300	chr22:29107968-29108686	HepG2	liver:	n/a	chr22:29108372-29108382
33	STAT3	chr22:29108245-29108781	MCF10A-Er-Src	breast:	n/a	chr22:29108269-29108292 chr22:29108269-29108277 chr22:29108530-29108538
34	ATF3	chr22:29108352-29108738	A549	lung:	n/a	n/a
35	CEBPB	chr22:29108257-29108827	HCT-116	colon:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539 chr22:29108258-29108269
36	BCL3	chr22:29108214-29108740	A549	lung:	n/a	n/a
37	CEBPB	chr22:29107889-29108729	A549	lung:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539 chr22:29108258-29108269
38	YY1	chr22:29108423-29108747	SK-N-SH_RA	brain:	n/a	n/a
39	BRCA1	chr22:29108040-29108805	Hela-S3	cervix:	n/a	n/a
40	STAT3	chr22:29108271-29108772	MCF10A-Er-Src	breast:	n/a	chr22:29108530-29108538
41	TCF12	chr22:29107720-29108859	SK-N-SH	brain:	n/a	n/a
42	CEBPB	chr22:29108214-29108682	K562	blood:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539 chr22:29108258-29108269
43	TCF12	chr22:29107763-29108946	A549	lung:	n/a	n/a
44	NFIC	chr22:29107954-29108655	HepG2	liver:	n/a	n/a
45	CEBPB	chr22:29108337-29108640	HCT-116	colon:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539
46	TEAD4	chr22:29107817-29108842	HepG2	liver:	n/a	n/a
47	TEAD4	chr22:29108315-29108771	A549	lung:	n/a	n/a
48	CEBPB	chr22:29108358-29108703	H1-hESC	embryonic stem cell:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539
49	FOS	chr22:29108086-29108781	MCF10A-Er-Src	breast:	n/a	n/a
50	CEBPB	chr22:29108439-29108591	K562	blood:	n/a	chr22:29108530-29108541 chr22:29108530-29108539 chr22:29108528-29108539

Variant related genes	Relation type
CHEK2	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1474961	0.90[CEU][hapmap]
rs16986509	0.81[CEU][hapmap]
rs17507066	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs17880353	0.91[YRI][hapmap]
rs17880459	0.91[YRI][hapmap]
rs17881056	0.91[YRI][hapmap]
rs17882607	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17884212	0.91[YRI][hapmap]
rs17885892	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788408	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762814	0.91[YRI][hapmap]
rs6005807	0.82[CEU][hapmap]
rs6005861	0.81[JPT][hapmap]
rs9620804	0.82[CEU][hapmap]
rs9625534	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs9625545	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625551	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv459867	chr22:28993183-29109036	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv588881	chr22:28993183-29109036	Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1064624	chr22:29065528-29130728	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv513775	chr22:29083731-29137822	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv517951	chr22:29105558-29135889	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29076200-29137600	Weak transcription	Esophagus	oesophagus
2	chr22:29076400-29119200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:29076400-29129400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr22:29079600-29130200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr22:29082200-29109800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr22:29082800-29137600	Weak transcription	Spleen	Spleen
7	chr22:29083000-29126600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:29085000-29116600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr22:29088600-29118600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr22:29090200-29129000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr22:29090400-29110800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:29090600-29137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:29090600-29137200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr22:29091000-29116600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:29091000-29120200	Weak transcription	Placenta	Placenta
16	chr22:29092000-29108600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:29093600-29121800	Weak transcription	Small Intestine	intestine
18	chr22:29093600-29132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr22:29093800-29126600	Weak transcription	Gastric	stomach
20	chr22:29094600-29125000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr22:29095200-29114600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr22:29097000-29130800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr22:29098800-29111400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr22:29099000-29109600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr22:29099400-29109800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr22:29099800-29129000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr22:29100400-29137200	Weak transcription	Pancreas	Pancrea
28	chr22:29101200-29118800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr22:29101600-29131000	Strong transcription	Dnd41	blood
30	chr22:29102400-29119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr22:29103400-29118800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr22:29103600-29114600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr22:29103600-29118800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr22:29103600-29124800	Weak transcription	GM12878-XiMat	blood
35	chr22:29103600-29132200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr22:29103800-29114800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr22:29104200-29116600	Weak transcription	Thymus	Thymus
38	chr22:29104400-29116600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:29104800-29116600	Weak transcription	Fetal Intestine Large	intestine
40	chr22:29105600-29110400	Strong transcription	Primary T cells from cord blood	blood
41	chr22:29105600-29137200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr22:29106000-29108800	Enhancers	Fetal Stomach	stomach
43	chr22:29106000-29109000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr22:29106000-29109000	Enhancers	NH-A	brain
45	chr22:29106000-29109200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr22:29106000-29129200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr22:29106200-29108600	Flanking Active TSS	NHDF-Ad	bronchial
48	chr22:29106400-29109200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr22:29106400-29110800	Weak transcription	Fetal Intestine Small	intestine
50	chr22:29106400-29114800	Weak transcription	Fetal Thymus	thymus

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