Variant report

Variant	rs58059561
Chromosome Location	chr2:98262402-98262403
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	chr2:98261488-98263007	A549	lung:	n/a	chr2:98262404-98262414
2	MXI1	chr2:98262180-98262784	Hela-S3	cervix:	n/a	n/a
3	MAX	chr2:98261796-98262937	ECC-1	luminal epithelium:	n/a	chr2:98262404-98262414
4	POLR2A	chr2:98261981-98262850	HepG2	liver:	n/a	n/a
5	MAX	chr2:98261994-98262636	SK-N-SH	brain:	n/a	chr2:98262404-98262414
6	POLR2A	chr2:98262029-98262822	GM12892	blood:	n/a	n/a
7	REST	chr2:98262109-98262837	HepG2	liver:	n/a	n/a
8	YY1	chr2:98262148-98262730	GM12891	blood:	n/a	chr2:98262338-98262347 chr2:98262403-98262412
9	SIN3AK20	chr2:98261557-98263138	MCF-7	breast:	n/a	n/a
10	TAF1	chr2:98261905-98262943	ECC-1	luminal epithelium:	n/a	n/a
11	SMARCB1	chr2:98261862-98262984	Hela-S3	cervix:	n/a	n/a
12	PML	chr2:98261735-98262858	MCF-7	breast:	n/a	n/a
13	POLR2A	chr2:98262003-98262949	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr2:98261353-98263086	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr2:98262050-98262823	Hela-S3	cervix:	n/a	n/a
16	YY1	chr2:98262329-98262839	ECC-1	luminal epithelium:	n/a	chr2:98262338-98262347 chr2:98262403-98262412
17	CTCF	chr2:98262260-98262410	HBMEC	blood vessel:	n/a	n/a
18	SIN3AK20	chr2:98262158-98262654	HepG2	liver:	n/a	n/a
19	CEBPB	chr2:98262155-98262761	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:98262081-98262788	Hela-S3	cervix:	n/a	n/a
21	RCOR1	chr2:98261745-98262708	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:98261643-98262759	K562	blood:	n/a	n/a
23	CEBPB	chr2:98262204-98262696	HepG2	liver:	n/a	n/a
24	IRF1	chr2:98261721-98262750	K562	blood:	n/a	chr2:98262017-98262028 chr2:98262334-98262348 chr2:98261945-98261959
25	TCF12	chr2:98262100-98262559	A549	lung:	n/a	n/a
26	PML	chr2:98261912-98262821	K562	blood:	n/a	n/a
27	POLR2A	chr2:98261896-98262788	ECC-1	luminal epithelium:	n/a	n/a
28	TBP	chr2:98262119-98262722	Hela-S3	cervix:	n/a	n/a
29	RUNX3	chr2:98261735-98262732	GM12878	blood:	n/a	n/a
30	RFX5	chr2:98262177-98262904	GM12878	blood:	n/a	n/a
31	TAF1	chr2:98262267-98262865	GM12892	blood:	n/a	n/a
32	POLR2A	chr2:98261758-98262934	HepG2	liver:	n/a	n/a
33	TEAD4	chr2:98261932-98262632	K562	blood:	n/a	n/a
34	TBL1XR1	chr2:98261773-98262747	GM12878	blood:	n/a	n/a
35	TAF1	chr2:98262071-98262771	PFSK-1	brain:	n/a	n/a
36	MAX	chr2:98262120-98262667	H1-hESC	embryonic stem cell:	n/a	chr2:98262404-98262414
37	MAX	chr2:98261600-98262815	NB4	blood:	n/a	chr2:98262404-98262414
38	TAF1	chr2:98262083-98262912	GM12878	blood:	n/a	n/a
39	CTCF	chr2:98262280-98262430	HEEpiC	esophagus:	n/a	n/a
40	GABPA	chr2:98262346-98262628	Hela-S3	cervix:	n/a	chr2:98262386-98262397 chr2:98262383-98262397 chr2:98262386-98262400
41	YY1	chr2:98262205-98262709	HCT-116	colon:	n/a	chr2:98262338-98262347 chr2:98262403-98262412
42	POLR2A	chr2:98261821-98262934	GM12878	blood:	n/a	n/a
43	MAX	chr2:98261888-98262871	GM12878	blood:	n/a	chr2:98262404-98262414
44	ARID3A	chr2:98262236-98262507	K562	blood:	n/a	n/a
45	GABPA	chr2:98262108-98262968	A549	lung:	n/a	chr2:98262386-98262397 chr2:98262383-98262397 chr2:98262338-98262347 chr2:98262386-98262400
46	TCF7L2	chr2:98261984-98262680	HCT-116	colon:	n/a	n/a
47	POLR2A	chr2:98261715-98262942	GM12892	blood:	n/a	n/a
48	POLR2A	chr2:98262016-98262834	HUVEC	blood vessel:	n/a	n/a
49	MAX	chr2:98262303-98262915	H1-hESC	embryonic stem cell:	n/a	chr2:98262404-98262414
50	POLR2A	chr2:98261542-98263124	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:98261015..98264268-chr2:98289158..98291782,3	K562	blood:
2	chr2:98260499..98265219-chr2:98284794..98288071,4	MCF-7	breast:
3	chr1:211752053..211752664-chr2:98262083..98262626,2	HCT-116	colon:
4	chr2:98262245..98265084-chr2:98284240..98286100,2	K562	blood:
5	chr2:98204043..98208769-chr2:98260858..98263741,4	MCF-7	breast:
6	chr17:48943638..48944526-chr2:98262048..98262634,2	HCT-116	colon:

Variant related genes	Relation type
COX5B	TF binding region
ENSG00000170385	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000196912	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000228486	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10460480	1.00[AMR][1000 genomes]
rs17022096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022495	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028435	1.00[AMR][1000 genomes]
rs17028568	1.00[AMR][1000 genomes]
rs17028640	1.00[AMR][1000 genomes]
rs17031009	1.00[AMR][1000 genomes]
rs2167008	1.00[AMR][1000 genomes]
rs55637939	1.00[AMR][1000 genomes]
rs56045386	1.00[AMR][1000 genomes]
rs56381875	1.00[AMR][1000 genomes]
rs56717024	1.00[AMR][1000 genomes]
rs56894046	1.00[AMR][1000 genomes]
rs57002448	1.00[AMR][1000 genomes]
rs57183691	1.00[AMR][1000 genomes]
rs57875000	1.00[AMR][1000 genomes]
rs58753916	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59134572	1.00[AMR][1000 genomes]
rs59340312	1.00[AMR][1000 genomes]
rs60599690	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60713338	1.00[AMR][1000 genomes]
rs61016336	1.00[AMR][1000 genomes]
rs61085184	0.94[AFR][1000 genomes]
rs72951140	1.00[AMR][1000 genomes]
rs73959761	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73959772	1.00[AMR][1000 genomes]
rs9678135	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv431402	chr2:97669032-98281634	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv535831	chr2:97671335-98270990	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	esv2752937	chr2:97708611-98269110	Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	esv2756939	chr2:97708611-98274527	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv2763630	chr2:97731133-98279050	Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv431413	chr2:97753585-98274527	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv522486	chr2:97768178-98265491	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv869602	chr2:97820572-98263438	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv1005903	chr2:97872625-98264679	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv999118	chr2:97886322-98264679	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv1011958	chr2:97886322-98269110	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv1001249	chr2:97972600-98274527	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv1005846	chr2:97972600-98281634	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
16	nsv1010905	chr2:98013814-98269110	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv1003384	chr2:98013814-98270884	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv1010167	chr2:98013814-98273619	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv999627	chr2:98013814-98274527	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv1009263	chr2:98013814-98281634	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 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	chr2:98261400-98263200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr2:98261400-98263400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:98261400-98263400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:98261400-98263400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:98261400-98263400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr2:98261400-98263400	Active TSS	Brain Angular Gyrus	brain
7	chr2:98261400-98263400	Active TSS	Fetal Brain Female	brain
8	chr2:98261400-98263400	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr2:98261400-98263600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr2:98261400-98263600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:98261400-98263800	Active TSS	Right Ventricle	heart
12	chr2:98261600-98262600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:98261600-98263200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:98261600-98263200	Active TSS	Aorta	Aorta
15	chr2:98261600-98263200	Active TSS	Lung	lung
16	chr2:98261600-98263400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:98261600-98263400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:98261600-98263400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr2:98261600-98263400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:98261600-98263400	Active TSS	Brain Substantia Nigra	brain
21	chr2:98261600-98263600	Active TSS	H1 Cell Line	embryonic stem cell
22	chr2:98261600-98263600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr2:98261600-98263600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:98261600-98263600	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr2:98261600-98263600	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr2:98261600-98263600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr2:98261600-98263600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr2:98261600-98263600	Active TSS	Right Atrium	heart
29	chr2:98261800-98263000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:98261800-98263200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:98261800-98263200	Active TSS	Placenta Amnion	Placenta Amnion
32	chr2:98261800-98263200	Active TSS	Thymus	Thymus
33	chr2:98261800-98263400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:98261800-98263400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:98261800-98263400	Active TSS	Brain Cingulate Gyrus	brain
36	chr2:98261800-98263400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:98261800-98263400	Active TSS	Colonic Mucosa	Colon
38	chr2:98261800-98263400	Active TSS	Colon Smooth Muscle	Colon
39	chr2:98261800-98263400	Active TSS	Fetal Kidney	kidney
40	chr2:98261800-98263400	Active TSS	Ovary	ovary
41	chr2:98261800-98263400	Active TSS	Pancreas	Pancrea
42	chr2:98261800-98263400	Active TSS	Psoas Muscle	Psoas
43	chr2:98261800-98263400	Active TSS	Stomach Mucosa	stomach
44	chr2:98261800-98263400	Active TSS	Osteobl	bone
45	chr2:98261800-98263600	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr2:98261800-98263600	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr2:98261800-98263600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr2:98261800-98263600	Active TSS	Left Ventricle	heart
49	chr2:98261800-98263600	Active TSS	Small Intestine	intestine
50	chr2:98261800-98263800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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