Variant report

Variant	rs11147724
Chromosome Location	chr13:39260659-39260660
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	YY1	chr13:39260573-39260933	H1-hESC	embryonic stem cell:	n/a	chr13:39260834-39260843 chr13:39260638-39260649
2	POLR2A	chr13:39260409-39261686	ECC-1	luminal epithelium:	n/a	n/a
3	CHD2	chr13:39260502-39262120	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
4	TBP	chr13:39260348-39262065	H1-hESC	embryonic stem cell:	n/a	n/a
5	CREB1	chr13:39260492-39261483	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr13:39260084-39260714	T-47D	breast:	n/a	chr13:39260616-39260632
7	NFYB	chr13:39260495-39260702	GM12878	blood:	n/a	chr13:39260570-39260585 chr13:39260570-39260585 chr13:39260570-39260584
8	E2F4	chr13:39260619-39261253	MCF10A-Er-Src	breast:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
9	RAD21	chr13:39259907-39260702	MCF-7	breast:	n/a	n/a
10	GTF2F1	chr13:39260601-39261588	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr13:39260206-39261986	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
12	ESR1	chr13:39260043-39260682	T-47D	breast:	n/a	n/a
13	SIN3AK20	chr13:39260053-39260966	MCF-7	breast:	n/a	n/a
14	SIN3A	chr13:39260139-39262313	H1-hESC	embryonic stem cell:	n/a	chr13:39261307-39261320
15	TEAD4	chr13:39260102-39260747	MCF-7	breast:	n/a	n/a
16	RAD21	chr13:39260029-39260720	MCF-7	breast:	n/a	n/a
17	POLR2A	chr13:39260556-39261638	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOXA1	chr13:39260088-39260730	T-47D	breast:	n/a	n/a
19	SIN3AK20	chr13:39259931-39261825	MCF-7	breast:	n/a	n/a
20	TAF1	chr13:39260458-39261731	H1-hESC	embryonic stem cell:	n/a	n/a
21	GATA3	chr13:39260044-39260728	T-47D	breast:	n/a	n/a
22	MAX	chr13:39260091-39261370	MCF-7	breast:	n/a	chr13:39260787-39260796
23	JUND	chr13:39260083-39260750	T-47D	breast:	n/a	chr13:39260574-39260583 chr13:39260520-39260532
24	EP300	chr13:39260143-39260664	T-47D	breast:	n/a	chr13:39260616-39260632
25	PML	chr13:39260162-39260755	MCF-7	breast:	n/a	n/a
26	SETDB1	chr13:39260078-39261495	U2OS	brain:	n/a	n/a
27	FOXM1	chr13:39260104-39260750	MCF-7	breast:	n/a	n/a
28	POLR2A	chr13:39260314-39262185	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr13:39260515-39261439	H1-hESC	embryonic stem cell:	n/a	chr13:39260834-39260843 chr13:39261291-39261302 chr13:39261309-39261323 chr13:39260638-39260649 chr13:39261294-39261308
30	SRF	chr13:39260121-39260871	MCF-7	breast:	n/a	n/a
31	ZNF143	chr13:39260139-39262011	H1-hESC	embryonic stem cell:	n/a	chr13:39261180-39261198 chr13:39261345-39261355
32	JUND	chr13:39260064-39260688	T-47D	breast:	n/a	chr13:39260574-39260583 chr13:39260520-39260532
33	MAX	chr13:39260345-39262000	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
34	E2F6	chr13:39260491-39262274	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
35	MAX	chr13:39260171-39261492	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796
36	FOXA1	chr13:39260112-39260669	T-47D	breast:	n/a	n/a
37	RAD21	chr13:39260033-39260739	ECC-1	luminal epithelium:	n/a	n/a
38	KAP1	chr13:39260290-39261341	U2OS	brain:	n/a	n/a
39	ZNF263	chr13:39260638-39262432	HEK293-T-REx	kidney:	n/a	chr13:39261113-39261122 chr13:39261031-39261040
40	NR2F2	chr13:39260096-39260719	MCF-7	breast:	n/a	n/a
41	MAX	chr13:39260086-39261151	MCF-7	breast:	n/a	chr13:39260787-39260796
42	RAD21	chr13:39260063-39261429	H1-hESC	embryonic stem cell:	n/a	n/a
43	EP300	chr13:39260117-39260721	MCF-7	breast:	n/a	chr13:39260616-39260632
44	GATA3	chr13:39259974-39260777	MCF-7	breast:	n/a	n/a
45	CTBP2	chr13:39260245-39262457	H1-hESC	embryonic stem cell:	n/a	n/a
46	FOXM1	chr13:39259936-39260785	MCF-7	breast:	n/a	n/a
47	MAX	chr13:39260425-39262136	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796
48	GATA3	chr13:39259943-39260931	MCF-7	breast:	n/a	chr13:39259962-39259972
49	HA-E2F1	chr13:39260257-39261857	MCF-7	breast:	n/a	chr13:39260302-39260316 chr13:39261047-39261061
50	MAX	chr13:39260631-39262256	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:39260633-39260683	U87	brain:	n/a
2	chr13:39260633-39260683	HCPEpiC	choroid plexus:	n/a
3	chr13:39260633-39260683	HNPCEpiC	eye:	n/a
4	chr13:39260633-39260683	GM12878	blood:	n/a
5	chr13:39260633-39260683	MCF-7	breast:	n/a
6	chr13:39260633-39260683	NH-A	brain:	n/a
7	chr13:39260633-39260683	CMK	blood:	n/a
8	chr13:39260633-39260683	SK-N-SH_RA	brain:	n/a
9	chr13:39260633-39260683	HRPEpiC	eye:	n/a
10	chr13:39260633-39260683	NHDF-neo	bronchial:	n/a
11	chr13:39260633-39260683	PrEC	prostate:	n/a
12	chr13:39260633-39260683	HMEC	breast:	n/a
13	chr13:39260633-39260683	H1-hESC	embryonic stem cell:	embryo
14	chr13:39260633-39260683	PANC-1	pancreas:	n/a
15	chr13:39260633-39260683	AG09319	gingival:	n/a
16	chr13:39260633-39260683	Hela-S3	cervix:	n/a
17	chr13:39260633-39260683	NT2-D1	testis:	n/a
18	chr13:39260633-39260683	BE2_C	brain:	n/a
19	chr13:39260633-39260683	HEK293	kidney:	embryo
20	chr13:39260633-39260683	HL-60	blood:	n/a
21	chr13:39260633-39260683	NB4	blood:	n/a
22	chr13:39260633-39260683	SAEC	small airway:	n/a
23	chr13:39260633-39260683	SK-N-SH	brain:	n/a
24	chr13:39260633-39260683	AG04449	skin:	fetal
25	chr13:39260633-39260683	MCF10A-Er-Src	breast:	n/a
26	chr13:39260633-39260683	HUVEC	blood vessel:	n/a
27	chr13:39260633-39260683	HRE	kidney:	n/a
28	chr13:39260633-39260683	HRCEpiC	kidney:	n/a
29	chr13:39260633-39260683	GM12891	blood:	n/a
30	chr13:39260633-39260683	Jurkat	blood:	n/a
31	chr13:39260633-39260683	HCT-116	colon:	n/a
32	chr13:39260633-39260683	SKMC	muscle:	n/a
33	chr13:39260633-39260683	HPAEpiC	pulmonary alveolar:	n/a
34	chr13:39260633-39260683	GM12892	blood:	n/a
35	chr13:39260633-39260683	GM06990	blood:	n/a
36	chr13:39260633-39260683	IMR90	lung:	fetal
37	chr13:39260633-39260683	BJ	skin:	n/a
38	chr13:39260633-39260683	PFSK-1	brain:	n/a
39	chr13:39260633-39260683	HEEpiC	esophagus:	n/a
40	chr13:39260633-39260683	AG10803	skin:	n/a
41	chr13:39260633-39260683	GM19239	blood:	n/a
42	chr13:39260633-39260683	AG04450	lung:	fetal
43	chr13:39260633-39260683	A549	lung:	n/a
44	chr13:39260633-39260683	SK-N-MC	brain:	n/a
45	chr13:39260633-39260683	HepG2	liver:	n/a
46	chr13:39260633-39260683	ovcar-3	ovarian:	n/a
47	chr13:39260633-39260683	Hepatocyte	liver:	n/a
48	chr13:39260633-39260683	K562	blood:	n/a
49	chr13:39260633-39260683	T-47D	breast:	n/a
50	chr13:39260633-39260683	HCM	heart:	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:39256386..39258055-chr13:39258985..39261054,2	MCF-7	breast:
2	chr13:39260551..39262193-chr6:28047138..28049723,2	MCF-7	breast:
3	chr13:39251483..39253844-chr13:39259100..39260979,2	MCF-7	breast:
4	chr13:39259930..39261837-chr13:39400225..39402249,2	MCF-7	breast:
5	chr13:39259853..39260679-chr13:39446387..39447489,3	MCF-7	breast:
6	chr13:39258919..39260831-chr13:39305195..39307479,2	MCF-7	breast:
7	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:
8	chr13:39259811..39260806-chr13:39337692..39338863,8	MCF-7	breast:
9	chr13:39255037..39256959-chr13:39258816..39261083,2	MCF-7	breast:

Variant related genes	Relation type
FREM2	TF binding region
FREM2	CpG island
ENSG00000225350	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11147723	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11147725	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17244358	0.93[EUR][1000 genomes]
rs2053848	0.93[EUR][1000 genomes]
rs2122208	0.89[EUR][1000 genomes]
rs2197879	0.89[EUR][1000 genomes]
rs2442335	0.91[EUR][1000 genomes]
rs2442339	0.91[EUR][1000 genomes]
rs2442340	0.89[EUR][1000 genomes]
rs2442341	0.83[EUR][1000 genomes]
rs2442343	0.89[EUR][1000 genomes]
rs2442344	0.90[EUR][1000 genomes]
rs2442373	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs2442379	0.89[EUR][1000 genomes]
rs2496418	0.89[EUR][1000 genomes]
rs2496419	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2496420	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2496425	0.91[EUR][1000 genomes]
rs2496430	0.85[AMR][1000 genomes]
rs2496433	0.83[AMR][1000 genomes]
rs35378642	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4329795	0.94[EUR][1000 genomes]
rs55860060	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55880170	0.83[AMR][1000 genomes]
rs55922882	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6563629	0.92[EUR][1000 genomes]
rs7331440	0.93[EUR][1000 genomes]
rs7991701	0.93[EUR][1000 genomes]
rs895895	0.93[EUR][1000 genomes]
rs930659	0.89[EUR][1000 genomes]
rs930660	0.93[EUR][1000 genomes]
rs9566354	0.94[EUR][1000 genomes]
rs9576589	0.93[EUR][1000 genomes]
rs9576590	0.93[EUR][1000 genomes]
rs9576591	0.92[EUR][1000 genomes]
rs9576592	0.92[EUR][1000 genomes]
rs9576595	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9634754	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs9788341	0.95[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11147724	CCNA1	cis	parietal	SCAN
rs11147724	CSNK1A1L	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39259600-39261800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr13:39259600-39262000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr13:39259800-39260800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr13:39259800-39261400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr13:39259800-39262000	Active TSS	Fetal Kidney	kidney
6	chr13:39260000-39261000	Active TSS	Fetal Intestine Large	intestine
7	chr13:39260000-39261600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr13:39260000-39261600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:39260000-39261800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr13:39260000-39261800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:39260000-39261800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr13:39260000-39261800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr13:39260000-39261800	Active TSS	Aorta	Aorta
14	chr13:39260000-39262000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr13:39260000-39262000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:39260000-39262000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr13:39260000-39262200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr13:39260000-39262200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr13:39260000-39262200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:39260200-39260800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:39260200-39260800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr13:39260200-39260800	Flanking Active TSS	HMEC	breast
23	chr13:39260200-39260800	Bivalent/Poised TSS	HSMMtube	muscle
24	chr13:39260200-39260800	Flanking Active TSS	NHEK	skin
25	chr13:39260200-39261200	Active TSS	Brain Cingulate Gyrus	brain
26	chr13:39260200-39261400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr13:39260200-39261400	Active TSS	Ovary	ovary
28	chr13:39260200-39261400	Active TSS	Right Ventricle	heart
29	chr13:39260200-39261600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
30	chr13:39260200-39261600	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr13:39260200-39261800	Flanking Active TSS	Liver	Liver
32	chr13:39260200-39261800	Active TSS	Brain Hippocampus Middle	brain
33	chr13:39260200-39262000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr13:39260200-39262000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr13:39260200-39262000	Active TSS	Fetal Heart	heart
36	chr13:39260200-39262000	Active TSS	Psoas Muscle	Psoas
37	chr13:39260200-39262200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:39260200-39262200	Active TSS	Brain Angular Gyrus	brain
39	chr13:39260200-39262200	Active TSS	Brain Substantia Nigra	brain
40	chr13:39260200-39262200	Active TSS	Rectal Smooth Muscle	rectum
41	chr13:39260200-39262200	Active TSS	Right Atrium	heart
42	chr13:39260200-39262400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:39260200-39262400	Active TSS	H9 Cell Line	embryonic stem cell
44	chr13:39260200-39262400	Active TSS	Brain Anterior Caudate	brain
45	chr13:39260200-39262400	Active TSS	Colon Smooth Muscle	Colon
46	chr13:39260400-39260800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:39260400-39260800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
48	chr13:39260400-39260800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr13:39260400-39260800	Bivalent/Poised TSS	GM12878-XiMat	blood
50	chr13:39260400-39260800	Bivalent Enhancer	HUVEC	blood vessel

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