Variant report

Variant	rs16988062
Chromosome Location	chr22:30209816-30209817
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	CTCF	chr22:30209600-30209891	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr22:30209657-30209858	MCF-7	breast:	n/a	n/a
3	RAD21	chr22:30209604-30209931	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr22:30209680-30209830	HUVEC	blood vessel:	n/a	n/a
5	CTCF	chr22:30209720-30209870	Caco-2	colon:	n/a	n/a
6	CTCF	chr22:30209740-30209890	HPF	lung:	n/a	n/a
7	CTCF	chr22:30209660-30209910	AG04449	skin:	n/a	n/a
8	MAX	chr22:30209481-30210412	MCF-7	breast:	n/a	chr22:30210078-30210087 chr22:30210077-30210088 chr22:30210078-30210088 chr22:30210077-30210088 chr22:30210079-30210086 chr22:30210073-30210092 chr22:30210078-30210087
9	RAD21	chr22:30209550-30209947	A549	lung:	n/a	n/a
10	CTCF	chr22:30209700-30209850	HCPEpiC	choroid plexus:	n/a	n/a
11	FOSL2	chr22:30209599-30209886	A549	lung:	n/a	n/a
12	CTCF	chr22:30209657-30209852	Hela-S3	cervix:	n/a	n/a
13	JUND	chr22:30209525-30209903	Hela-S3	cervix:	n/a	chr22:30209710-30209721
14	NR2F2	chr22:30209532-30209904	K562	blood:	n/a	n/a
15	CTCF	chr22:30209740-30209890	HBMEC	blood vessel:	n/a	n/a
16	RCOR1	chr22:30209569-30209833	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr22:30209700-30209850	Hela-S3	cervix:	n/a	n/a
18	FOSL2	chr22:30209481-30209976	A549	lung:	n/a	n/a
19	CTCF	chr22:30209680-30209830	BJ	skin:	n/a	n/a
20	FOS	chr22:30209576-30209896	MCF10A-Er-Src	breast:	n/a	n/a
21	CTCF	chr22:30209661-30209878	K562	blood:	n/a	n/a
22	CTCF	chr22:30209720-30209870	HCFaa	heart:	n/a	n/a
23	CTCF	chr22:30209669-30209928	K562	blood:	n/a	n/a
24	CTCF	chr22:30209635-30209834	A549	lung:	n/a	n/a
25	RCOR1	chr22:30209643-30209889	K562	blood:	n/a	n/a
26	MYC	chr22:30209670-30210154	MCF10A-Er-Src	breast:	n/a	chr22:30210078-30210087 chr22:30210077-30210088 chr22:30210078-30210088 chr22:30210077-30210088 chr22:30210079-30210086 chr22:30210073-30210092 chr22:30210078-30210087
27	JUND	chr22:30209557-30210251	HepG2	liver:	n/a	chr22:30209710-30209721
28	CTCF	chr22:30209680-30209830	HVMF	connective:	n/a	n/a
29	CTCF	chr22:30209780-30209930	GM12871	blood:	n/a	n/a
30	BHLHE40	chr22:30209626-30210228	K562	blood:	n/a	n/a
31	CTCF	chr22:30209700-30209850	HEK293	kidney:	n/a	n/a
32	CTCF	chr22:30209658-30209847	Gliobla	brain:	n/a	n/a
33	NR2F2	chr22:30209173-30210392	MCF-7	breast:	n/a	n/a
34	CTCF	chr22:30209680-30209830	HMF	breast:	n/a	n/a
35	SMC3	chr22:30209590-30209913	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr22:30209740-30209890	Hela-S3	cervix:	n/a	n/a
37	GATA3	chr22:30209396-30210503	MCF-7	breast:	n/a	n/a
38	CTCF	chr22:30209700-30209850	HRPEpiC	eye:	n/a	n/a
39	MYC	chr22:30209628-30209859	MCF10A-Er-Src	breast:	n/a	n/a
40	FOS	chr22:30209544-30209926	MCF10A-Er-Src	breast:	n/a	n/a
41	CTCF	chr22:30209720-30209870	HMF	breast:	n/a	n/a
42	RAD21	chr22:30209666-30209842	K562	blood:	n/a	n/a
43	CTCF	chr22:30209671-30209867	HUVEC	blood vessel:	n/a	n/a
44	CTCF	chr22:30209720-30209870	HPAF	blood vessel:	n/a	n/a
45	CTCF	chr22:30209680-30209830	AoAF	blood vessel:	n/a	n/a
46	RAD21	chr22:30209617-30209861	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr22:30209680-30209830	SAEC	small airway:	n/a	n/a
48	JUND	chr22:30209546-30210096	K562	blood:	n/a	chr22:30209710-30209721
49	CTCF	chr22:30209680-30209830	MCF-7	breast:	n/a	n/a
50	CTCF	chr22:30209410-30210305	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30209515..30211458-chr22:30232926..30235230,2	K562	blood:
2	chr22:30192738..30197507-chr22:30207918..30212414,7	MCF-7	breast:
3	chr22:30198973..30201297-chr22:30207957..30210741,2	MCF-7	breast:
4	chr22:30208243..30210090-chr22:30279066..30280884,2	MCF-7	breast:
5	chr22:30206160..30207800-chr22:30209309..30211288,2	K562	blood:

Variant related genes	Relation type
ASCC2	TF binding region
ENSG00000100325	Chromatin interaction
ENSG00000100330	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11090582	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12166580	1.00[EUR][1000 genomes]
rs12627866	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16988011	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16988043	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16988044	1.00[EUR][1000 genomes]
rs56783715	1.00[EUR][1000 genomes]
rs58113244	1.00[EUR][1000 genomes]
rs58538392	1.00[EUR][1000 genomes]
rs58643523	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59172206	1.00[EUR][1000 genomes]
rs59237579	1.00[EUR][1000 genomes]
rs59422664	1.00[EUR][1000 genomes]
rs59542747	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs5997520	0.87[YRI][hapmap]
rs60020246	1.00[EUR][1000 genomes]
rs6006241	0.81[AFR][1000 genomes]
rs60965931	1.00[EUR][1000 genomes]
rs61432554	1.00[EUR][1000 genomes]
rs7286724	1.00[EUR][1000 genomes]
rs7290848	1.00[EUR][1000 genomes]
rs73392899	0.88[AFR][1000 genomes]
rs73394816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73394842	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs740116	0.81[YRI][hapmap]
rs9620930	1.00[EUR][1000 genomes]
rs9620939	1.00[EUR][1000 genomes]
rs9625869	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9625890	1.00[EUR][1000 genomes]
rs9625903	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30182200-30217000	Strong transcription	Fetal Intestine Small	intestine
3	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
4	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
5	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
6	chr22:30183000-30221400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr22:30183400-30224000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr22:30183800-30224000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr22:30184000-30222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:30191000-30222200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr22:30193400-30217200	Strong transcription	Fetal Thymus	thymus
15	chr22:30194200-30212200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr22:30195400-30222000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr22:30195400-30222200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr22:30196000-30212000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr22:30196000-30217000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr22:30196200-30211800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr22:30196200-30215400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr22:30196200-30217200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr22:30196200-30217200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr22:30196400-30211800	Strong transcription	Placenta	Placenta
27	chr22:30196400-30221200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr22:30197000-30222200	Strong transcription	Dnd41	blood
29	chr22:30197400-30216000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr22:30197400-30216200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr22:30198000-30211800	Strong transcription	Left Ventricle	heart
32	chr22:30198200-30211800	Weak transcription	Right Atrium	heart
33	chr22:30199200-30211800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr22:30199200-30222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr22:30199400-30211000	Strong transcription	Right Ventricle	heart
36	chr22:30199400-30211800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr22:30200600-30211400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr22:30203000-30211000	Strong transcription	Fetal Muscle Leg	muscle
39	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr22:30204000-30214200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr22:30204200-30217000	Weak transcription	Fetal Heart	heart
42	chr22:30205800-30211200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr22:30205800-30211200	Strong transcription	Ovary	ovary
44	chr22:30205800-30211400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr22:30205800-30211800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr22:30205800-30211800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr22:30205800-30211800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr22:30205800-30212000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr22:30205800-30212000	Strong transcription	Brain Hippocampus Middle	brain
50	chr22:30205800-30215800	Strong transcription	Aorta	Aorta

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