Variant report

Variant	rs12057708
Chromosome Location	chr1:223895793-223895794
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	MAFF	chr1:223895792-223896002	HepG2	liver:	n/a	n/a
2	GATA3	chr1:223894647-223895914	SK-N-SH	brain:	n/a	chr1:223895582-223895592 chr1:223895089-223895098
3	TCF12	chr1:223894790-223895924	ECC-1	luminal epithelium:	n/a	n/a
4	E2F4	chr1:223894924-223896020	MCF10A-Er-Src	breast:	n/a	n/a
5	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
6	STAT3	chr1:223894869-223895978	MCF10A-Er-Src	breast:	n/a	n/a
7	TEAD4	chr1:223895632-223896084	HepG2	liver:	n/a	n/a
8	CEBPB	chr1:223894954-223896073	A549	lung:	n/a	n/a
9	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
10	TBP	chr1:223894867-223895953	Hela-S3	cervix:	n/a	n/a
11	HDAC2	chr1:223895605-223896026	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:223894932-223896021	MCF10A-Er-Src	breast:	n/a	n/a
13	REST	chr1:223894826-223895919	A549	lung:	n/a	n/a
14	POLR2A	chr1:223894783-223896133	HCT-116	colon:	n/a	n/a
15	TCF7L2	chr1:223894836-223895872	HCT-116	colon:	n/a	chr1:223895087-223895096
16	SMARCC1	chr1:223894761-223895863	Hela-S3	cervix:	n/a	chr1:223895061-223895070 chr1:223895088-223895097
17	RCOR1	chr1:223893645-223896056	IMR90	lung:	n/a	n/a
18	HNF4A	chr1:223895611-223896077	HepG2	liver:	n/a	chr1:223895851-223895866
19	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
20	SIN3AK20	chr1:223894718-223896189	HCT-116	colon:	n/a	n/a
21	POLR2A	chr1:223894919-223896036	HCT-116	colon:	n/a	n/a
22	BCL3	chr1:223894647-223896166	A549	lung:	n/a	n/a
23	PBX3	chr1:223894707-223895881	SK-N-SH	brain:	n/a	n/a
24	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
25	MAZ	chr1:223894762-223896017	IMR90	lung:	n/a	n/a
26	POLR2A	chr1:223895122-223895946	Hela-S3	cervix:	n/a	n/a
27	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
28	CTCF	chr1:223895760-223895910	WI-38	lung:	n/a	n/a
29	TCF12	chr1:223892902-223896167	A549	lung:	n/a	chr1:223893770-223893780
30	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
31	JUND	chr1:223895660-223896005	HepG2	liver:	n/a	n/a
32	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
33	POLR2A	chr1:223894809-223896090	HUVEC	blood vessel:	n/a	n/a
34	MAFK	chr1:223895749-223895949	HepG2	liver:	n/a	n/a
35	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
36	ZNF143	chr1:223894879-223895887	K562	blood:	n/a	n/a
37	MAZ	chr1:223895717-223895984	HepG2	liver:	n/a	n/a
38	CEBPB	chr1:223895670-223896073	HepG2	liver:	n/a	n/a
39	MAX	chr1:223894835-223895983	Hela-S3	cervix:	n/a	n/a
40	MAZ	chr1:223894890-223895831	K562	blood:	n/a	n/a
41	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
42	SP1	chr1:223895698-223896016	HepG2	liver:	n/a	chr1:223895705-223895726 chr1:223895700-223895709 chr1:223895698-223895710
43	HNF4G	chr1:223895558-223896056	HepG2	liver:	n/a	chr1:223895857-223895872
44	FOXA2	chr1:223894740-223896059	A549	lung:	n/a	n/a
45	CTCF	chr1:223895740-223895890	GM12873	blood:	n/a	n/a
46	STAT3	chr1:223894901-223895987	MCF10A-Er-Src	breast:	n/a	n/a
47	CTCF	chr1:223895780-223895930	HVMF	connective:	n/a	n/a
48	EP300	chr1:223894692-223895977	SK-N-SH	brain:	n/a	n/a
49	EP300	chr1:223893634-223896045	A549	lung:	n/a	chr1:223894428-223894442
50	SIX5	chr1:223893446-223895984	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223895202..223897591-chr1:223904463..223906328,2	K562	blood:
2	chr1:223887828..223890332-chr1:223892364..223895816,5	K562	blood:
3	chr1:223895536..223897944-chr1:223933865..223935699,2	MCF-7	breast:
4	chr1:223894371..223897139-chr1:224032420..224034876,4	MCF-7	breast:
5	chr1:223893260..223897061-chr1:223935259..223940090,6	MCF-7	breast:
6	chr1:223891443..223896975-chr1:223925207..223929791,6	MCF-7	breast:
7	chr1:223693305..223695548-chr1:223894201..223896140,2	MCF-7	breast:
8	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
9	chr1:223893459..223896572-chr1:223897626..223901997,6	K562	blood:
10	chr1:223895060..223897000-chr1:223946083..223948413,2	MCF-7	breast:
11	chr1:223895463..223896414-chr1:223936797..223937493,2	MCF-7	breast:
12	chr1:223892791..223896772-chr1:223919510..223922888,4	MCF-7	breast:

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10916576	0.83[AMR][1000 genomes]
rs10916601	0.88[ASN][1000 genomes]
rs10916602	0.88[ASN][1000 genomes]
rs10916604	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579787	0.81[AMR][1000 genomes]
rs11580689	0.81[AMR][1000 genomes]
rs12074091	0.88[ASN][1000 genomes]
rs12080565	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16842040	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1892077	0.88[ASN][1000 genomes]
rs2000320	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154113	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2154114	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2186006	0.88[ASN][1000 genomes]
rs2275877	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28370012	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28370013	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28370014	0.88[ASN][1000 genomes]
rs28370020	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4653499	0.88[ASN][1000 genomes]
rs61823966	0.88[ASN][1000 genomes]
rs7366009	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7414311	0.88[ASN][1000 genomes]
rs7555491	0.88[ASN][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	chr1:223889000-223900000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:223891200-223898600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:223892000-223897000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:223892200-223895800	Enhancers	Fetal Lung	lung
5	chr1:223892200-223895800	Enhancers	Right Ventricle	heart
6	chr1:223892200-223896000	Enhancers	Left Ventricle	heart
7	chr1:223892200-223899800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:223892400-223895800	Enhancers	Rectal Smooth Muscle	rectum
9	chr1:223892400-223896800	Enhancers	Placenta	Placenta
10	chr1:223892400-223897000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:223892400-223897000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:223892400-223897000	Enhancers	Fetal Muscle Leg	muscle
13	chr1:223892400-223898400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:223892600-223895800	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:223892600-223895800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:223892600-223896000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:223892600-223896000	Enhancers	Fetal Stomach	stomach
18	chr1:223892600-223896200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:223892600-223897000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:223892800-223896000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:223892800-223896000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:223893000-223898800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:223893200-223895800	Enhancers	Brain Anterior Caudate	brain
24	chr1:223893200-223896200	Enhancers	Right Atrium	heart
25	chr1:223893400-223899600	Weak transcription	Fetal Kidney	kidney
26	chr1:223893600-223897000	Enhancers	Fetal Muscle Trunk	muscle
27	chr1:223893800-223895800	Enhancers	Colon Smooth Muscle	Colon
28	chr1:223893800-223896000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:223893800-223898200	Enhancers	Fetal Heart	heart
30	chr1:223894000-223896000	Enhancers	Fetal Intestine Small	intestine
31	chr1:223894000-223896000	Enhancers	Pancreas	Pancrea
32	chr1:223894000-223896000	Enhancers	Placenta Amnion	Placenta Amnion
33	chr1:223894000-223897000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:223894000-223898600	Weak transcription	Fetal Brain Female	brain
35	chr1:223894000-223899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:223894000-223899800	Enhancers	Fetal Intestine Large	intestine
37	chr1:223894200-223896000	Enhancers	Spleen	Spleen
38	chr1:223894600-223898600	Weak transcription	Brain Germinal Matrix	brain
39	chr1:223894600-223899000	Weak transcription	Fetal Brain Male	brain
40	chr1:223895000-223895800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:223895000-223895800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr1:223895000-223895800	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr1:223895000-223895800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr1:223895000-223895800	Flanking Active TSS	K562	blood
45	chr1:223895000-223896000	Enhancers	Ovary	ovary
46	chr1:223895000-223896000	Flanking Active TSS	Hela-S3	cervix
47	chr1:223895000-223896000	Flanking Active TSS	NHDF-Ad	bronchial
48	chr1:223895000-223896000	Flanking Active TSS	NHEK	skin
49	chr1:223895200-223895800	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr1:223895200-223895800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links