Variant report

Variant	rs9613859
Chromosome Location	chr22:29703409-29703410
allele	C/G
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	ELF1	chr22:29702497-29703476	K562	blood:	n/a	n/a
2	POLR2A	chr22:29703239-29703836	K562	blood:	n/a	n/a
3	CTCF	chr22:29703400-29703550	HCM	heart:	n/a	n/a
4	MAZ	chr22:29702058-29703657	Hela-S3	cervix:	n/a	chr22:29702885-29702895
5	RCOR1	chr22:29703103-29703457	HepG2	liver:	n/a	n/a
6	MAX	chr22:29701922-29703739	A549	lung:	n/a	chr22:29702885-29702895
7	HCFC1	chr22:29703407-29703463	K562	blood:	n/a	n/a
8	TCF12	chr22:29701819-29703578	ECC-1	luminal epithelium:	n/a	chr22:29702870-29702878 chr22:29702992-29703000 chr22:29702074-29702084
9	POLR2A	chr22:29702090-29703706	SK-N-MC	brain:	n/a	n/a
10	ZNF143	chr22:29703000-29703977	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr22:29703320-29703470	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr22:29702046-29703418	Hela-S3	cervix:	n/a	chr22:29702885-29702895
13	CTCF	chr22:29701947-29703979	SK-N-SH	brain:	n/a	chr22:29702302-29702315
14	RCOR1	chr22:29702974-29704037	Hela-S3	cervix:	n/a	n/a
15	HDAC2	chr22:29702735-29703721	MCF-7	breast:	n/a	n/a
16	ZNF143	chr22:29703015-29703636	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr22:29701917-29703687	HepG2	liver:	n/a	chr22:29702885-29702895
18	RCOR1	chr22:29702939-29703568	K562	blood:	n/a	n/a
19	MAX	chr22:29701829-29703686	ECC-1	luminal epithelium:	n/a	chr22:29702885-29702895
20	TAF1	chr22:29702736-29703415	ECC-1	luminal epithelium:	n/a	n/a
21	MYC	chr22:29702808-29703571	MCF10A-Er-Src	breast:	n/a	chr22:29702885-29702895
22	TFAP2C	chr22:29701978-29703656	Hela-S3	cervix:	n/a	n/a
23	TFAP2A	chr22:29702017-29703655	Hela-S3	cervix:	n/a	chr22:29702828-29702839 chr22:29702567-29702578
24	CTCF	chr22:29703340-29703490	AG09319	gingival:	n/a	n/a
25	ZC3H11A	chr22:29703407-29703569	K562	blood:	n/a	n/a
26	MAX	chr22:29701938-29703824	MCF-7	breast:	n/a	chr22:29702885-29702895
27	ZNF143	chr22:29703110-29703556	K562	blood:	n/a	n/a
28	CHD2	chr22:29703352-29703411	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr22:29701924-29703608	A549	lung:	n/a	chr22:29702302-29702315
30	CTCF	chr22:29703300-29703450	SK-N-SH_RA	brain:	n/a	n/a
31	CTCF	chr22:29703400-29703550	SAEC	small airway:	n/a	n/a
32	NR3C1	chr22:29702122-29703468	A549	lung:	n/a	chr22:29702406-29702419 chr22:29702664-29702680 chr22:29702661-29702682 chr22:29702664-29702680 chr22:29702665-29702679
33	ZKSCAN1	chr22:29702894-29703621	Hela-S3	cervix:	n/a	n/a
34	MYC	chr22:29702085-29703581	K562	blood:	n/a	chr22:29702885-29702895
35	POLR2A	chr22:29702158-29703439	K562	blood:	n/a	n/a
36	RCOR1	chr22:29701922-29704280	IMR90	lung:	n/a	n/a
37	MAZ	chr22:29702782-29703424	HepG2	liver:	n/a	chr22:29702885-29702895
38	POLR2A	chr22:29702012-29703701	K562	blood:	n/a	n/a
39	POLR2A	chr22:29702818-29703665	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr22:29701873-29703448	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr22:29702136-29703618	IMR90	lung:	n/a	n/a
42	TCF12	chr22:29703209-29703618	A549	lung:	n/a	n/a
43	MYC	chr22:29702090-29703529	K562	blood:	n/a	chr22:29702885-29702895
44	POLR2A	chr22:29702763-29703481	ProgFib	skin:	n/a	n/a
45	CCNT2	chr22:29702139-29703480	K562	blood:	n/a	n/a
46	MAZ	chr22:29701830-29704170	IMR90	lung:	n/a	chr22:29702885-29702895
47	SIN3AK20	chr22:29702716-29703411	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr22:29702071-29703445	ECC-1	luminal epithelium:	n/a	n/a
49	ZBTB7A	chr22:29702062-29703717	ECC-1	luminal epithelium:	n/a	chr22:29702934-29702941 chr22:29702825-29702833
50	MXI1	chr22:29702552-29703514	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29702549..29705407-chr22:29734900..29738437,3	MCF-7	breast:
2	chr22:29661955..29666922-chr22:29700529..29704114,10	K562	blood:
3	chr22:29660929..29666447-chr22:29700529..29705135,9	K562	blood:
4	chr22:29700857..29704420-chr22:29708764..29712339,6	MCF-7	breast:
5	chr22:29703109..29706869-chr22:29711325..29716000,5	K562	blood:
6	chr22:29685583..29688004-chr22:29700889..29703726,2	MCF-7	breast:
7	chr22:29701804..29704290-chr22:29781998..29785634,5	MCF-7	breast:
8	chr22:29663358..29665751-chr22:29702504..29704805,4	MCF-7	breast:
9	chr22:29702481..29704174-chr22:29874105..29876353,2	K562	blood:

Variant related genes	Relation type
GAS2L1	TF binding region
ENSG00000225465	Chromatin interaction
ENSG00000100285	Chromatin interaction
ENSG00000100276	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000100280	Chromatin interaction
ENSG00000273216	Chromatin interaction
ENSG00000182944	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2002566	0.81[ASN][1000 genomes]
rs2267135	0.84[ASN][1000 genomes]
rs2301291	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2301586	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2348468	0.81[ASN][1000 genomes]
rs2857466	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2881921	0.80[ASN][1000 genomes]
rs34234634	0.81[ASN][1000 genomes]
rs378720	0.81[ASN][1000 genomes]
rs3788412	0.84[ASN][1000 genomes]
rs4823032	0.87[ASN][1000 genomes]
rs5752906	0.82[ASN][1000 genomes]
rs5763144	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763171	0.81[ASN][1000 genomes]
rs5763172	0.84[ASN][1000 genomes]
rs5763173	0.81[ASN][1000 genomes]
rs5763179	0.81[ASN][1000 genomes]
rs5763182	0.81[ASN][1000 genomes]
rs5763184	0.81[ASN][1000 genomes]
rs5763189	0.80[ASN][1000 genomes]
rs5763190	0.80[ASN][1000 genomes]
rs5997467	0.81[ASN][1000 genomes]
rs6006103	0.83[ASN][1000 genomes]
rs6006108	0.80[ASN][1000 genomes]
rs6006109	0.80[ASN][1000 genomes]
rs6006112	0.81[ASN][1000 genomes]
rs6006113	0.81[ASN][1000 genomes]
rs6006115	0.84[ASN][1000 genomes]
rs737883	0.90[ASN][1000 genomes]
rs909798	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv829155	chr22:29664396-29724001	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS 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 target site	21 gene(s)	inside rSNPs	diseases
5	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
6	nsv914959	chr22:29696438-29712874	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv914960	chr22:29696438-29714069	Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29702000-29703600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr22:29702000-29703600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr22:29702000-29703600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr22:29702000-29703600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
5	chr22:29702000-29703800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr22:29702000-29704000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr22:29702000-29704000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:29702000-29704400	Flanking Active TSS	Colonic Mucosa	Colon
9	chr22:29702000-29705600	Active TSS	Fetal Brain Female	brain
10	chr22:29702000-29707800	Enhancers	Fetal Heart	heart
11	chr22:29702200-29703600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:29702200-29703600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr22:29702200-29703600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr22:29702200-29703600	Active TSS	Muscle Satellite Cultured Cells	--
15	chr22:29702200-29703600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr22:29702200-29703600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr22:29702200-29703600	Active TSS	Duodenum Mucosa	Duodenum
18	chr22:29702200-29703600	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr22:29702200-29703600	Active TSS	Esophagus	oesophagus
20	chr22:29702200-29703600	Active TSS	Psoas Muscle	Psoas
21	chr22:29702200-29703600	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr22:29702200-29703600	Active TSS	Rectal Smooth Muscle	rectum
23	chr22:29702200-29703600	Bivalent/Poised TSS	Thymus	Thymus
24	chr22:29702200-29703600	Active TSS	Hela-S3	cervix
25	chr22:29702200-29703600	Active TSS	HUVEC	blood vessel
26	chr22:29702200-29703800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr22:29702200-29703800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr22:29702200-29703800	Active TSS	Brain Substantia Nigra	brain
29	chr22:29702200-29703800	Active TSS	Fetal Kidney	kidney
30	chr22:29702200-29703800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr22:29702200-29703800	Active TSS	NHDF-Ad	bronchial
32	chr22:29702200-29704000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:29702200-29704000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr22:29702200-29704000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr22:29702200-29704000	Active TSS	Right Ventricle	heart
36	chr22:29702200-29704200	Active TSS	A549	lung
37	chr22:29702200-29704600	Active TSS	Brain Anterior Caudate	brain
38	chr22:29702400-29703600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr22:29702400-29703600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr22:29702400-29703600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr22:29702400-29703600	Active TSS	Colon Smooth Muscle	Colon
42	chr22:29702400-29703600	Active TSS	Left Ventricle	heart
43	chr22:29702400-29703600	Active TSS	Lung	lung
44	chr22:29702400-29703800	Active TSS	Primary T cells from cord blood	blood
45	chr22:29702400-29703800	Active TSS	Aorta	Aorta
46	chr22:29702400-29703800	Active TSS	NHLF	lung
47	chr22:29702400-29704000	Active TSS	HSMMtube	muscle
48	chr22:29702600-29703600	Active TSS	Brain Angular Gyrus	brain
49	chr22:29702600-29703600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr22:29702600-29703600	Active TSS	Placenta Amnion	Placenta Amnion

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