Variant report

Variant	rs12724682
Chromosome Location	chr1:113256368-113256369
allele	C/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	ESR1	chr1:113256015-113256554	T-47D	breast:	n/a	chr1:113256338-113256355
2	ESR1	chr1:113255960-113256678	ECC-1	luminal epithelium:	n/a	chr1:113256338-113256355
3	ESR1	chr1:113256049-113256539	T-47D	breast:	n/a	chr1:113256338-113256355
4	MTA3	chr1:113256339-113257049	GM12878	blood:	n/a	n/a
5	CTCF	chr1:113256340-113256490	HEK293	kidney:	n/a	chr1:113256365-113256378
6	CTBP2	chr1:113256344-113257826	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF217	chr1:113256153-113256622	MCF-7	breast:	n/a	n/a
8	SIN3A	chr1:113256279-113259295	H1-hESC	embryonic stem cell:	n/a	chr1:113258039-113258050
9	ESR1	chr1:113256143-113256479	T-47D	breast:	n/a	chr1:113256338-113256355
10	ESR1	chr1:113256089-113256508	ECC-1	luminal epithelium:	n/a	chr1:113256338-113256355
11	ESR1	chr1:113256094-113256546	T-47D	breast:	n/a	chr1:113256338-113256355
12	ZBTB7A	chr1:113256120-113257937	ECC-1	luminal epithelium:	n/a	n/a
13	ESR1	chr1:113255942-113256688	ECC-1	luminal epithelium:	n/a	chr1:113256338-113256355
14	ESR1	chr1:113256004-113256667	ECC-1	luminal epithelium:	n/a	chr1:113256338-113256355
15	ESR1	chr1:113256060-113256471	T-47D	breast:	n/a	chr1:113256338-113256355
16	ESR1	chr1:113256117-113256438	T-47D	breast:	n/a	chr1:113256338-113256355
17	SPI1	chr1:113256302-113257405	GM12878	blood:	n/a	chr1:113256637-113256650 chr1:113256490-113256503
18	ESR1	chr1:113256051-113256584	ECC-1	luminal epithelium:	n/a	chr1:113256338-113256355
19	ESR1	chr1:113256082-113256539	ECC-1	luminal epithelium:	n/a	chr1:113256338-113256355
20	HDAC2	chr1:113256106-113256521	MCF-7	breast:	n/a	n/a
21	TCF12	chr1:113256074-113256783	ECC-1	luminal epithelium:	n/a	chr1:113256444-113256454
22	NFIC	chr1:113256034-113256736	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113160555..113166228-chr1:113255932..113262161,8	K562	blood:
2	chr1:113160602..113163896-chr1:113252357..113259247,7	K562	blood:
3	chr1:113215712..113221627-chr1:113253708..113259381,5	MCF-7	breast:
4	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
5	chr1:113256258..113258254-chr1:113933817..113936025,2	K562	blood:
6	chr1:113255626..113260544-chr1:113496476..113500122,4	K562	blood:
7	chr1:113166528..113169223-chr1:113253776..113256616,2	MCF-7	breast:
8	chr1:113166467..113169316-chr1:113256023..113257569,2	K562	blood:
9	chr1:113215800..113219074-chr1:113254460..113258669,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261595	TF binding region
PPM1J	TF binding region
ENSG00000271810	TF binding region
ENSG00000155380	Chromatin interaction
ENSG00000081026	Chromatin interaction
ENSG00000226419	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12722725	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722910	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729635	1.00[ASN][1000 genomes]
rs12736457	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737053	1.00[ASN][1000 genomes]
rs34611728	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34731458	1.00[ASN][1000 genomes]
rs34961977	1.00[ASN][1000 genomes]
rs351366	1.00[ASN][1000 genomes]
rs35735679	1.00[ASN][1000 genomes]
rs35995150	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36087180	1.00[ASN][1000 genomes]
rs61818824	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61818825	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61818828	1.00[ASN][1000 genomes]
rs6688050	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71659381	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv872157	chr1:113247467-113265819	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv547566	chr1:113248365-113301657	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv872158	chr1:113250888-113265819	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv872159	chr1:113252091-113265819	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113249000-113256400	Weak transcription	Fetal Heart	heart
2	chr1:113250400-113256400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:113250400-113256600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:113250400-113256600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:113250400-113256600	Weak transcription	Psoas Muscle	Psoas
6	chr1:113250400-113256800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:113250400-113256800	Weak transcription	Aorta	Aorta
8	chr1:113250600-113256600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:113250600-113256800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:113250600-113257000	Weak transcription	HUVEC	blood vessel
11	chr1:113250800-113256600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:113250800-113256600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:113250800-113256600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:113250800-113256600	Weak transcription	Osteobl	bone
15	chr1:113251000-113256400	Weak transcription	NHEK	skin
16	chr1:113251000-113257200	Weak transcription	Hela-S3	cervix
17	chr1:113251400-113256800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:113253400-113256400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:113254400-113256400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:113254600-113257200	Weak transcription	Dnd41	blood
21	chr1:113255200-113256600	Enhancers	Brain Hippocampus Middle	brain
22	chr1:113255400-113256400	Bivalent Enhancer	HepG2	liver
23	chr1:113255600-113256400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:113255600-113256400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:113255800-113256400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr1:113255800-113256400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:113255800-113256400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:113255800-113256600	Enhancers	Liver	Liver
29	chr1:113256000-113256400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:113256000-113256400	Enhancers	GM12878-XiMat	blood
31	chr1:113256000-113256600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:113256000-113256600	Enhancers	Brain Anterior Caudate	brain
33	chr1:113256000-113256600	Enhancers	Brain Substantia Nigra	brain
34	chr1:113256000-113256600	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr1:113256000-113256600	Enhancers	Right Ventricle	heart
36	chr1:113256000-113256600	Enhancers	Stomach Mucosa	stomach
37	chr1:113256000-113256600	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr1:113256000-113256800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
39	chr1:113256000-113256800	Enhancers	Primary B cells from peripheral blood	blood
40	chr1:113256000-113256800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:113256000-113256800	Enhancers	Placenta	Placenta
42	chr1:113256000-113256800	Bivalent Enhancer	Fetal Thymus	thymus
43	chr1:113256000-113256800	Enhancers	Left Ventricle	heart
44	chr1:113256000-113256800	Enhancers	Lung	lung
45	chr1:113256000-113257000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr1:113256000-113257400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:113256200-113256400	Enhancers	Right Atrium	heart
48	chr1:113256200-113256600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
49	chr1:113256200-113256600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:113256200-113256600	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links