Variant report

Variant	rs60780652
Chromosome Location	chr22:29168360-29168361
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	YY1	chr22:29168257-29169323	GM12892	blood:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
2	MYBL2	chr22:29168334-29168857	HepG2	liver:	n/a	n/a
3	MBD4	chr22:29168336-29168918	HepG2	liver:	n/a	n/a
4	MAX	chr22:29168340-29169061	HepG2	liver:	n/a	n/a
5	POLR2A	chr22:29168307-29169740	HUVEC	blood vessel:	n/a	n/a
6	ELF1	chr22:29168314-29169052	MCF-7	breast:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
7	MXI1	chr22:29168340-29170168	IMR90	lung:	n/a	n/a
8	TAF1	chr22:29168330-29168913	PFSK-1	brain:	n/a	n/a
9	ELF1	chr22:29168289-29168990	SK-N-SH	brain:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
10	YY1	chr22:29168353-29169075	GM12891	blood:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
11	YY1	chr22:29168284-29169165	K562	blood:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
12	POLR2A	chr22:29168296-29169662	H1-hESC	embryonic stem cell:	n/a	n/a
13	MTA3	chr22:29168198-29168967	GM12878	blood:	n/a	n/a
14	ELF1	chr22:29168219-29168931	HCT-116	colon:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
15	TCF12	chr22:29168323-29168950	A549	lung:	n/a	n/a
16	STAT3	chr22:29168348-29168773	GM12878	blood:	n/a	n/a
17	TBP	chr22:29168352-29169503	K562	blood:	n/a	n/a
18	YY1	chr22:29168348-29169194	H1-hESC	embryonic stem cell:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
19	TEAD4	chr22:29168336-29168827	K562	blood:	n/a	n/a
20	CREB1	chr22:29168336-29169044	GM12878	blood:	n/a	n/a
21	TBL1XR1	chr22:29168289-29168897	GM12878	blood:	n/a	n/a
22	YY1	chr22:29168244-29168936	A549	lung:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
23	ELF1	chr22:29168271-29169460	GM12878	blood:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
24	MAX	chr22:29168309-29169492	A549	lung:	n/a	n/a
25	YY1	chr22:29168247-29168910	SK-N-SH_RA	brain:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
26	CREB1	chr22:29168303-29169506	HepG2	liver:	n/a	n/a
27	RUNX3	chr22:29168314-29169061	GM12878	blood:	n/a	n/a
28	YY1	chr22:29168165-29169093	SK-N-SH	brain:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
29	ELF1	chr22:29168209-29168968	HCT-116	colon:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
30	ELF1	chr22:29168343-29168906	HepG2	liver:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
31	POLR2A	chr22:29168340-29169016	U87	brain:	n/a	n/a
32	CREB1	chr22:29168353-29168950	K562	blood:	n/a	n/a
33	REST	chr22:29168209-29169380	H1-neurons	neurons:	n/a	chr22:29168763-29168776
34	TCF12	chr22:29168356-29168915	ECC-1	luminal epithelium:	n/a	n/a
35	YY1	chr22:29168262-29169107	GM12878	blood:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
36	MXI1	chr22:29168262-29169923	SK-N-SH	brain:	n/a	n/a
37	YY1	chr22:29168308-29169030	GM12878	blood:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
38	PML	chr22:29168190-29170017	GM12878	blood:	n/a	chr22:29168555-29168563
39	ZNF143	chr22:29168251-29169872	GM12878	blood:	n/a	chr22:29168660-29168678 chr22:29168618-29168636
40	CBX3	chr22:29168313-29168810	K562	blood:	n/a	n/a
41	REST	chr22:29168236-29168951	HL-60	blood:	n/a	chr22:29168763-29168776
42	ELF1	chr22:29168318-29168857	SK-N-SH	brain:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
43	GTF3C2	chr22:29168190-29168719	Hela-S3	cervix:	n/a	n/a
44	YY1	chr22:29168263-29169465	HepG2	liver:	n/a	chr22:29169324-29169338 chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
45	ETS1	chr22:29168330-29168919	A549	lung:	n/a	chr22:29168616-29168629
46	RCOR1	chr22:29168358-29169045	GM12878	blood:	n/a	n/a
47	YY1	chr22:29168359-29168791	A549	lung:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168590-29168612 chr22:29168768-29168782
48	POLR2A	chr22:29168358-29169219	PFSK-1	brain:	n/a	n/a
49	SIN3AK20	chr22:29168264-29170161	MCF-7	breast:	n/a	n/a
50	RCOR1	chr22:29168351-29169760	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
2	chr22:29162785..29164822-chr22:29166459..29168547,3	MCF-7	breast:
3	chr22:29168270..29171327-chr22:29194850..29198169,6	MCF-7	breast:
4	chr22:29136431..29140671-chr22:29167494..29170117,5	K562	blood:
5	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
6	chr22:29167233..29170944-chr22:29195431..29200472,7	K562	blood:
7	chr22:29134226..29139597-chr22:29164663..29170736,9	K562	blood:
8	chr22:29135038..29141691-chr22:29167545..29172967,16	MCF-7	breast:
9	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
10	chr22:29134212..29140528-chr22:29167074..29172462,20	MCF-7	breast:
11	chr22:29167462..29171106-chr22:29208719..29213065,6	MCF-7	breast:

Variant related genes	Relation type
CCDC117	TF binding region
ENSG00000100219	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000272858	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11912894	1.00[EUR][1000 genomes]
rs11913224	1.00[EUR][1000 genomes]
rs11913805	1.00[EUR][1000 genomes]
rs17882995	1.00[EUR][1000 genomes]
rs55665300	1.00[EUR][1000 genomes]
rs55945584	1.00[EUR][1000 genomes]
rs56332784	1.00[EUR][1000 genomes]
rs57119189	1.00[EUR][1000 genomes]
rs57188271	1.00[EUR][1000 genomes]
rs57846969	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58089713	1.00[EUR][1000 genomes]
rs58162235	1.00[EUR][1000 genomes]
rs58579082	1.00[EUR][1000 genomes]
rs59519868	1.00[EUR][1000 genomes]
rs59546292	1.00[EUR][1000 genomes]
rs60003056	1.00[EUR][1000 genomes]
rs6005942	1.00[EUR][1000 genomes]
rs60155737	1.00[EUR][1000 genomes]
rs60187407	1.00[EUR][1000 genomes]
rs60747358	1.00[EUR][1000 genomes]
rs61257487	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61581392	1.00[EUR][1000 genomes]
rs722590	1.00[EUR][1000 genomes]
rs73430163	1.00[EUR][1000 genomes]
rs73430202	1.00[EUR][1000 genomes]
rs73881118	1.00[EUR][1000 genomes]
rs73881187	1.00[EUR][1000 genomes]
rs73881189	1.00[EUR][1000 genomes]
rs73881197	1.00[EUR][1000 genomes]
rs73881200	1.00[EUR][1000 genomes]
rs73881201	1.00[EUR][1000 genomes]
rs73882404	1.00[EUR][1000 genomes]
rs73882405	1.00[EUR][1000 genomes]
rs73882406	1.00[EUR][1000 genomes]
rs73882414	1.00[EUR][1000 genomes]
rs73882422	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29165800-29168600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:29167000-29168600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:29167200-29168400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr22:29167200-29168400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr22:29167200-29168400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr22:29167200-29168400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:29167600-29168400	Enhancers	Liver	Liver
8	chr22:29167600-29168400	Enhancers	Pancreas	Pancrea
9	chr22:29167600-29168400	Enhancers	HepG2	liver
10	chr22:29167600-29168600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:29167800-29168600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr22:29168000-29168400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr22:29168000-29168600	Weak transcription	Lung	lung
14	chr22:29168200-29168400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr22:29168200-29168400	Enhancers	Primary B cells from peripheral blood	blood
16	chr22:29168200-29168400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr22:29168200-29168400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr22:29168200-29168400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr22:29168200-29168400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr22:29168200-29168400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr22:29168200-29168400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr22:29168200-29168400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr22:29168200-29168400	Enhancers	Fetal Intestine Large	intestine
24	chr22:29168200-29168400	Enhancers	Fetal Muscle Trunk	muscle
25	chr22:29168200-29168400	Weak transcription	HMEC	breast
26	chr22:29168200-29168600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr22:29168200-29168600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr22:29168200-29168600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr22:29168200-29168600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr22:29168200-29168600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr22:29168200-29168600	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr22:29168200-29168600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr22:29168200-29168600	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr22:29168200-29168600	Enhancers	Fetal Thymus	thymus
35	chr22:29168200-29168600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr22:29168200-29168600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr22:29168200-29168600	Flanking Active TSS	Dnd41	blood
38	chr22:29168200-29168600	Flanking Active TSS	Hela-S3	cervix
39	chr22:29168200-29168600	Flanking Active TSS	NHEK	skin
40	chr22:29168200-29169400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr22:29168200-29169400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr22:29168200-29169400	Active TSS	Brain Angular Gyrus	brain
43	chr22:29168200-29169400	Active TSS	Brain Cingulate Gyrus	brain
44	chr22:29168200-29169400	Active TSS	Fetal Muscle Leg	muscle
45	chr22:29168200-29169400	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr22:29168200-29169400	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr22:29168200-29169600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr22:29168200-29169600	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr22:29168200-29169600	Active TSS	K562	blood
50	chr22:29168200-29169800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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