Variant report

Variant	rs62158266
Chromosome Location	chr2:98612799-98612800
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	MAX	chr2:98612222-98612905	K562	blood:	n/a	chr2:98612354-98612364 chr2:98612740-98612750 chr2:98612693-98612703
2	POLR2A	chr2:98612112-98613078	SK-N-SH	brain:	n/a	n/a
3	PML	chr2:98612058-98613038	MCF-7	breast:	n/a	n/a
4	REST	chr2:98612085-98613011	HepG2	liver:	n/a	chr2:98612629-98612642 chr2:98612209-98612229
5	POLR2A	chr2:98611450-98613099	GM18526	blood:	n/a	n/a
6	THAP1	chr2:98611742-98612992	K562	blood:	n/a	chr2:98612379-98612403 chr2:98612642-98612666
7	USF1	chr2:98612225-98612908	K562	blood:	n/a	chr2:98612742-98612758
8	CTCF	chr2:98612740-98612890	AG09319	gingival:	n/a	n/a
9	CEBPB	chr2:98612549-98612868	K562	blood:	n/a	n/a
10	TAF1	chr2:98612611-98613018	Hela-S3	cervix:	n/a	n/a
11	MAX	chr2:98611507-98613121	SK-N-SH	brain:	n/a	chr2:98612354-98612364 chr2:98612740-98612750 chr2:98612693-98612703
12	MAX	chr2:98612169-98613167	H1-hESC	embryonic stem cell:	n/a	chr2:98612354-98612364 chr2:98612740-98612750 chr2:98612693-98612703
13	POLR2A	chr2:98611493-98613168	K562	blood:	n/a	n/a
14	POLR2A	chr2:98611581-98613081	ECC-1	luminal epithelium:	n/a	n/a
15	EGR1	chr2:98612125-98613185	HCT-116	colon:	n/a	chr2:98612454-98612464 chr2:98612453-98612466 chr2:98612284-98612293 chr2:98612731-98612753 chr2:98612737-98612747 chr2:98612735-98612748 chr2:98612737-98612746 chr2:98612450-98612464 chr2:98612740-98612750 chr2:98612735-98612748 chr2:98612453-98612466 chr2:98612738-98612747 chr2:98612454-98612464 chr2:98612736-98612747 chr2:98612735-98612748 chr2:98612453-98612466 chr2:98612452-98612466 chr2:98612736-98612747 chr2:98612454-98612465 chr2:98612734-98612749 chr2:98612454-98612463 chr2:98612737-98612747 chr2:98612453-98612460 chr2:98612735-98612748 chr2:98612280-98612289 chr2:98612454-98612465 chr2:98612735-98612749
16	HMGN3	chr2:98611727-98612933	K562	blood:	n/a	n/a
17	FOXM1	chr2:98612164-98612937	GM12878	blood:	n/a	n/a
18	SP1	chr2:98612114-98613143	A549	lung:	n/a	chr2:98612740-98612749 chr2:98612431-98612440 chr2:98612429-98612441 chr2:98612750-98612761 chr2:98612431-98612440 chr2:98612430-98612439 chr2:98612739-98612751 chr2:98612739-98612750 chr2:98612740-98612750 chr2:98612739-98612751 chr2:98612519-98612533 chr2:98612430-98612440 chr2:98612741-98612750 chr2:98612426-98612440 chr2:98612740-98612750 chr2:98612429-98612441 chr2:98612430-98612440
19	HDAC2	chr2:98611469-98613023	HepG2	liver:	n/a	n/a
20	CTCF	chr2:98612720-98612870	AG04449	skin:	n/a	n/a
21	ZNF143	chr2:98612262-98612851	Hela-S3	cervix:	n/a	n/a
22	BRCA1	chr2:98612554-98613001	GM12878	blood:	n/a	n/a
23	ELK1	chr2:98612551-98612963	GM12878	blood:	n/a	n/a
24	RAD21	chr2:98612446-98613140	GM12878	blood:	n/a	chr2:98612508-98612518 chr2:98612506-98612518
25	NFYB	chr2:98612603-98612813	GM12878	blood:	n/a	n/a
26	NFATC1	chr2:98612328-98613061	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:98612023-98612990	A549	lung:	n/a	n/a
28	MAX	chr2:98611578-98613212	ECC-1	luminal epithelium:	n/a	chr2:98612354-98612364 chr2:98612740-98612750 chr2:98612693-98612703
29	ZNF143	chr2:98611888-98613041	H1-hESC	embryonic stem cell:	n/a	n/a
30	RCOR1	chr2:98612091-98612991	Hela-S3	cervix:	n/a	n/a
31	MAX	chr2:98612065-98613307	A549	lung:	n/a	chr2:98612354-98612364 chr2:98612740-98612750 chr2:98612693-98612703
32	TCF12	chr2:98612107-98612834	GM12878	blood:	n/a	chr2:98612471-98612478
33	FOS	chr2:98612655-98613020	MCF10A-Er-Src	breast:	n/a	chr2:98612947-98612957
34	POLR2A	chr2:98612566-98613003	SK-N-MC	brain:	n/a	n/a
35	POLR2A	chr2:98611683-98612967	A549	lung:	n/a	n/a
36	MAX	chr2:98612169-98613193	SK-N-SH	brain:	n/a	chr2:98612354-98612364 chr2:98612740-98612750 chr2:98612693-98612703
37	ELF1	chr2:98612458-98613088	K562	blood:	n/a	chr2:98612676-98612685
38	RFX5	chr2:98612648-98612829	K562	blood:	n/a	n/a
39	CREB1	chr2:98611524-98613194	HepG2	liver:	n/a	n/a
40	RELA	chr2:98611133-98613064	GM18505	blood:	n/a	n/a
41	POLR2A	chr2:98612146-98612993	HepG2	liver:	n/a	n/a
42	PAX5	chr2:98612077-98612879	GM12878	blood:	n/a	n/a
43	TAF1	chr2:98612162-98612893	H1-neurons	neurons:	n/a	n/a
44	ATF3	chr2:98612584-98612823	GM12878	blood:	n/a	n/a
45	TBP	chr2:98611697-98613052	H1-hESC	embryonic stem cell:	n/a	n/a
46	TAF1	chr2:98611694-98613102	H1-hESC	embryonic stem cell:	n/a	n/a
47	ZC3H11A	chr2:98612552-98613075	K562	blood:	n/a	n/a
48	TBP	chr2:98611525-98613040	HepG2	liver:	n/a	n/a
49	PML	chr2:98612528-98612919	GM12878	blood:	n/a	n/a
50	HEY1	chr2:98612652-98612996	K562	blood:	n/a	chr2:98612735-98612750 chr2:98612719-98612734

No.	Distal block	Cell Line	Cell type
1	chr2:98612119..98614854-chr2:98702248..98705786,3	K562	blood:
2	chr11:62609029..62609648-chr2:98612237..98612821,2	NB4	blood:
3	chr2:98523325..98524831-chr2:98610615..98613167,2	MCF-7	breast:
4	chr2:98610350..98614892-chr2:98700211..98704879,10	MCF-7	breast:

Variant related genes	Relation type
TMEM131	TF binding region
ENSG00000168658	Chromatin interaction
ENSG00000075568	Chromatin interaction
ENSG00000133316	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs55853292	0.88[EUR][1000 genomes]
rs58690282	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59049638	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59444417	0.89[EUR][1000 genomes]
rs59635122	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59752876	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61363543	0.82[EUR][1000 genomes]
rs62156482	0.82[EUR][1000 genomes]
rs62156488	0.88[EUR][1000 genomes]
rs62156507	0.86[EUR][1000 genomes]
rs62156508	0.89[EUR][1000 genomes]
rs62156509	0.89[EUR][1000 genomes]
rs62156514	0.82[EUR][1000 genomes]
rs62156519	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62156522	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62156523	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62156524	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62156525	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62156526	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156527	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62156530	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62158265	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62158268	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62158269	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62158270	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62158272	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73960433	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73960435	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7600204	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr2:98608600-98612800	Active TSS	GM12878-XiMat	blood
2	chr2:98609200-98613400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:98609400-98613000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:98609400-98613200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:98609800-98612800	Active TSS	NHLF	lung
6	chr2:98609800-98613200	Active TSS	Aorta	Aorta
7	chr2:98609800-98613400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:98610000-98612800	Active TSS	Fetal Muscle Trunk	muscle
9	chr2:98610000-98613000	Active TSS	Fetal Intestine Small	intestine
10	chr2:98610000-98613000	Active TSS	Fetal Stomach	stomach
11	chr2:98610000-98613200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:98610200-98612800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:98610200-98612800	Active TSS	Fetal Intestine Large	intestine
14	chr2:98610200-98613200	Active TSS	Colonic Mucosa	Colon
15	chr2:98610400-98613000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:98610400-98613200	Active TSS	Stomach Mucosa	stomach
17	chr2:98610400-98613400	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr2:98610400-98613400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:98610400-98613400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:98610600-98612800	Active TSS	Pancreas	Pancrea
21	chr2:98610600-98612800	Active TSS	Right Ventricle	heart
22	chr2:98610600-98612800	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr2:98610600-98612800	Active TSS	HMEC	breast
24	chr2:98610600-98612800	Active TSS	HSMM	muscle
25	chr2:98610600-98613000	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr2:98610600-98613000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:98610600-98613200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr2:98610600-98613200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:98610600-98613200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:98610600-98613200	Active TSS	Fetal Kidney	kidney
31	chr2:98610600-98613200	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr2:98610600-98613200	Active TSS	Fetal Lung	lung
33	chr2:98610600-98613200	Active TSS	Left Ventricle	heart
34	chr2:98610600-98613200	Active TSS	Ovary	ovary
35	chr2:98610600-98613200	Active TSS	A549	lung
36	chr2:98610600-98613200	Active TSS	HSMMtube	muscle
37	chr2:98610800-98612800	Active TSS	Primary B cells from peripheral blood	blood
38	chr2:98610800-98612800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:98610800-98612800	Active TSS	Fetal Muscle Leg	muscle
40	chr2:98610800-98612800	Active TSS	Fetal Thymus	thymus
41	chr2:98610800-98612800	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr2:98610800-98612800	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr2:98610800-98612800	Active TSS	NHDF-Ad	bronchial
44	chr2:98610800-98613000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr2:98610800-98613000	Active TSS	Muscle Satellite Cultured Cells	--
46	chr2:98610800-98613000	Active TSS	K562	blood
47	chr2:98610800-98613200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:98610800-98613200	Active TSS	Placenta Amnion	Placenta Amnion
49	chr2:98610800-98613200	Active TSS	Psoas Muscle	Psoas
50	chr2:98610800-98613200	Active TSS	Rectal Smooth Muscle	rectum

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