Variant report

Variant	rs61598725
Chromosome Location	chr1:223895367-223895368
allele	A/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	JUN	chr1:223894855-223895593	Hela-S3	cervix:	n/a	chr1:223895064-223895072 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
2	GATA3	chr1:223894647-223895914	SK-N-SH	brain:	n/a	chr1:223895582-223895592 chr1:223895089-223895098
3	JUND	chr1:223894803-223895634	Hela-S3	cervix:	n/a	chr1:223895059-223895070 chr1:223895064-223895072 chr1:223895086-223895097 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
4	FOS	chr1:223894857-223895672	K562	blood:	n/a	chr1:223895059-223895070 chr1:223895064-223895072 chr1:223895086-223895097 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
5	TCF12	chr1:223894790-223895924	ECC-1	luminal epithelium:	n/a	n/a
6	E2F4	chr1:223894924-223896020	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL2	chr1:223894793-223895678	SK-N-SH	brain:	n/a	chr1:223895064-223895072 chr1:223895059-223895071 chr1:223895087-223895098 chr1:223895087-223895097 chr1:223895060-223895071 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
8	FOS	chr1:223894847-223895973	MCF10A-Er-Src	breast:	n/a	chr1:223895059-223895070 chr1:223895064-223895072 chr1:223895086-223895097 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
9	STAT3	chr1:223894869-223895978	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr1:223894954-223896073	A549	lung:	n/a	n/a
11	JUN	chr1:223894871-223895808	K562	blood:	n/a	chr1:223895064-223895072 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
12	TBP	chr1:223894867-223895953	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:223894932-223896021	MCF10A-Er-Src	breast:	n/a	n/a
14	ATF3	chr1:223894675-223895471	A549	lung:	n/a	n/a
15	REST	chr1:223894826-223895919	A549	lung:	n/a	n/a
16	POLR2A	chr1:223894783-223896133	HCT-116	colon:	n/a	n/a
17	TEAD4	chr1:223894754-223895515	K562	blood:	n/a	n/a
18	TCF7L2	chr1:223894836-223895872	HCT-116	colon:	n/a	chr1:223895087-223895096
19	SMARCC1	chr1:223894761-223895863	Hela-S3	cervix:	n/a	chr1:223895061-223895070 chr1:223895088-223895097
20	RCOR1	chr1:223893645-223896056	IMR90	lung:	n/a	n/a
21	HDAC2	chr1:223894805-223895565	MCF-7	breast:	n/a	n/a
22	POLR2A	chr1:223895253-223895674	A549	lung:	n/a	n/a
23	FOS	chr1:223894804-223896030	MCF10A-Er-Src	breast:	n/a	chr1:223895059-223895070 chr1:223895064-223895072 chr1:223895086-223895097 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
24	SIN3AK20	chr1:223894718-223896189	HCT-116	colon:	n/a	n/a
25	USF1	chr1:223894709-223895507	A549	lung:	n/a	n/a
26	POLR2A	chr1:223894919-223896036	HCT-116	colon:	n/a	n/a
27	BCL3	chr1:223894647-223896166	A549	lung:	n/a	n/a
28	RAD21	chr1:223894853-223895754	IMR90	lung:	n/a	n/a
29	PBX3	chr1:223894707-223895881	SK-N-SH	brain:	n/a	n/a
30	JUND	chr1:223894800-223895803	A549	lung:	n/a	chr1:223895059-223895070 chr1:223895064-223895072 chr1:223895086-223895097 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
31	MAZ	chr1:223894762-223896017	IMR90	lung:	n/a	n/a
32	POLR2A	chr1:223895122-223895946	Hela-S3	cervix:	n/a	n/a
33	JUN	chr1:223894639-223895926	K562	blood:	n/a	chr1:223895064-223895072 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
34	PBX3	chr1:223894805-223895587	A549	lung:	n/a	n/a
35	TCF12	chr1:223892902-223896167	A549	lung:	n/a	chr1:223893770-223893780
36	FOSL1	chr1:223894744-223896114	HCT-116	colon:	n/a	chr1:223895064-223895072 chr1:223895059-223895071 chr1:223895086-223895097 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895059-223895070 chr1:223895061-223895069
37	FOS	chr1:223894813-223896111	MCF10A-Er-Src	breast:	n/a	chr1:223895059-223895070 chr1:223895064-223895072 chr1:223895086-223895097 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
38	GATA3	chr1:223894712-223895652	A549	lung:	n/a	chr1:223895582-223895592 chr1:223895089-223895098
39	POLR2A	chr1:223894809-223896090	HUVEC	blood vessel:	n/a	n/a
40	JUND	chr1:223894711-223895905	SK-N-SH	brain:	n/a	chr1:223895059-223895070 chr1:223895064-223895072 chr1:223895086-223895097 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
41	ZNF143	chr1:223894879-223895887	K562	blood:	n/a	n/a
42	MAX	chr1:223894896-223895577	ECC-1	luminal epithelium:	n/a	n/a
43	MAX	chr1:223894835-223895983	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:223894954-223895762	Hela-S3	cervix:	n/a	n/a
45	MAZ	chr1:223894890-223895831	K562	blood:	n/a	n/a
46	FOS	chr1:223894795-223895837	HUVEC	blood vessel:	n/a	chr1:223895059-223895070 chr1:223895064-223895072 chr1:223895086-223895097 chr1:223895059-223895071 chr1:223895087-223895097 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069
47	UBTF	chr1:223894988-223895788	K562	blood:	n/a	n/a
48	FOXA2	chr1:223894740-223896059	A549	lung:	n/a	n/a
49	STAT3	chr1:223894901-223895987	MCF10A-Er-Src	breast:	n/a	n/a
50	FOSL2	chr1:223894755-223895708	A549	lung:	n/a	chr1:223895064-223895072 chr1:223895059-223895071 chr1:223895087-223895098 chr1:223895087-223895097 chr1:223895060-223895071 chr1:223895088-223895096 chr1:223895086-223895098 chr1:223895087-223895097 chr1:223895061-223895069

No.	Distal block	Cell Line	Cell type
1	chr1:223895202..223897591-chr1:223904463..223906328,2	K562	blood:
2	chr1:223895120..223895623-chr9:123604912..123605540,2	Hela-S3	cervix:
3	chr1:223887828..223890332-chr1:223892364..223895816,5	K562	blood:
4	chr1:223893369..223895448-chr1:223913219..223916092,2	K562	blood:
5	chr1:223894371..223897139-chr1:224032420..224034876,4	MCF-7	breast:
6	chr1:223893260..223897061-chr1:223935259..223940090,6	MCF-7	breast:
7	chr1:223891443..223896975-chr1:223925207..223929791,6	MCF-7	breast:
8	chr1:223894556..223895508-chr10:14920264..14921010,2	HCT-116	colon:
9	chr1:223693305..223695548-chr1:223894201..223896140,2	MCF-7	breast:
10	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
11	chr1:223893459..223896572-chr1:223897626..223901997,6	K562	blood:
12	chr1:223895060..223897000-chr1:223946083..223948413,2	MCF-7	breast:
13	chr1:223892791..223896772-chr1:223919510..223922888,4	MCF-7	breast:

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000152455	Chromatin interaction
ENSG00000143514	Chromatin interaction
ENSG00000095261	Chromatin interaction
ENSG00000162909	Chromatin interaction
ENSG00000272853	Chromatin interaction
ENSG00000226752	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12137025	0.86[AFR][1000 genomes]
rs12137149	0.86[AFR][1000 genomes]
rs55854109	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223889000-223895400	Enhancers	NHLF	lung
2	chr1:223889000-223900000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223891000-223895400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:223891200-223898600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:223892000-223897000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:223892200-223895600	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:223892200-223895800	Enhancers	Fetal Lung	lung
8	chr1:223892200-223895800	Enhancers	Right Ventricle	heart
9	chr1:223892200-223896000	Enhancers	Left Ventricle	heart
10	chr1:223892200-223899800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:223892400-223895400	Enhancers	Adipose Nuclei	Adipose
12	chr1:223892400-223895800	Enhancers	Rectal Smooth Muscle	rectum
13	chr1:223892400-223896800	Enhancers	Placenta	Placenta
14	chr1:223892400-223897000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:223892400-223897000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:223892400-223897000	Enhancers	Fetal Muscle Leg	muscle
17	chr1:223892400-223898400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:223892600-223895400	Enhancers	Stomach Mucosa	stomach
19	chr1:223892600-223895600	Enhancers	Brain Substantia Nigra	brain
20	chr1:223892600-223895800	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:223892600-223895800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr1:223892600-223896000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:223892600-223896000	Enhancers	Fetal Stomach	stomach
24	chr1:223892600-223896200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:223892600-223897000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:223892800-223895400	Weak transcription	Esophagus	oesophagus
27	chr1:223892800-223896000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:223892800-223896000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:223893000-223898800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:223893200-223895600	Enhancers	Brain Hippocampus Middle	brain
31	chr1:223893200-223895800	Enhancers	Brain Anterior Caudate	brain
32	chr1:223893200-223896200	Enhancers	Right Atrium	heart
33	chr1:223893400-223899600	Weak transcription	Fetal Kidney	kidney
34	chr1:223893600-223897000	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:223893800-223895800	Enhancers	Colon Smooth Muscle	Colon
36	chr1:223893800-223896000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:223893800-223898200	Enhancers	Fetal Heart	heart
38	chr1:223894000-223895400	Weak transcription	Gastric	stomach
39	chr1:223894000-223896000	Enhancers	Fetal Intestine Small	intestine
40	chr1:223894000-223896000	Enhancers	Pancreas	Pancrea
41	chr1:223894000-223896000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:223894000-223897000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:223894000-223898600	Weak transcription	Fetal Brain Female	brain
44	chr1:223894000-223899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:223894000-223899800	Enhancers	Fetal Intestine Large	intestine
46	chr1:223894200-223896000	Enhancers	Spleen	Spleen
47	chr1:223894400-223895400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:223894400-223895400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:223894400-223895400	Weak transcription	Psoas Muscle	Psoas
50	chr1:223894600-223895400	Active TSS	A549	lung

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