Variant report

Variant	rs11147725
Chromosome Location	chr13:39260738-39260739
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	SP1	chr13:39260679-39261399	H1-hESC	embryonic stem cell:	n/a	chr13:39261037-39261046 chr13:39261030-39261041 chr13:39260835-39260849
2	YY1	chr13:39260573-39260933	H1-hESC	embryonic stem cell:	n/a	chr13:39260834-39260843 chr13:39260638-39260649
3	POLR2A	chr13:39260409-39261686	ECC-1	luminal epithelium:	n/a	n/a
4	CHD2	chr13:39260502-39262120	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
5	MXI1	chr13:39260671-39261714	H1-hESC	embryonic stem cell:	n/a	n/a
6	TBP	chr13:39260348-39262065	H1-hESC	embryonic stem cell:	n/a	n/a
7	CREB1	chr13:39260492-39261483	H1-hESC	embryonic stem cell:	n/a	n/a
8	CHD1	chr13:39260721-39261618	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
9	E2F4	chr13:39260619-39261253	MCF10A-Er-Src	breast:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
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	SIN3AK20	chr13:39260053-39260966	MCF-7	breast:	n/a	n/a
13	SIN3A	chr13:39260139-39262313	H1-hESC	embryonic stem cell:	n/a	chr13:39261307-39261320
14	TEAD4	chr13:39260102-39260747	MCF-7	breast:	n/a	n/a
15	POLR2A	chr13:39260556-39261638	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3AK20	chr13:39259931-39261825	MCF-7	breast:	n/a	n/a
17	TAF1	chr13:39260458-39261731	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr13:39260091-39261370	MCF-7	breast:	n/a	chr13:39260787-39260796
19	JUND	chr13:39260083-39260750	T-47D	breast:	n/a	chr13:39260574-39260583 chr13:39260520-39260532
20	PML	chr13:39260162-39260755	MCF-7	breast:	n/a	n/a
21	SETDB1	chr13:39260078-39261495	U2OS	brain:	n/a	n/a
22	FOXM1	chr13:39260104-39260750	MCF-7	breast:	n/a	n/a
23	POLR2A	chr13:39260314-39262185	H1-hESC	embryonic stem cell:	n/a	n/a
24	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
25	SRF	chr13:39260121-39260871	MCF-7	breast:	n/a	n/a
26	ZNF143	chr13:39260139-39262011	H1-hESC	embryonic stem cell:	n/a	chr13:39261180-39261198 chr13:39261345-39261355
27	MAX	chr13:39260345-39262000	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
28	E2F6	chr13:39260491-39262274	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
29	MAX	chr13:39260171-39261492	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796
30	RAD21	chr13:39260033-39260739	ECC-1	luminal epithelium:	n/a	n/a
31	KAP1	chr13:39260290-39261341	U2OS	brain:	n/a	n/a
32	E2F6	chr13:39260737-39262112	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
33	ZNF263	chr13:39260638-39262432	HEK293-T-REx	kidney:	n/a	chr13:39261113-39261122 chr13:39261031-39261040
34	MAX	chr13:39260086-39261151	MCF-7	breast:	n/a	chr13:39260787-39260796
35	RAD21	chr13:39260063-39261429	H1-hESC	embryonic stem cell:	n/a	n/a
36	GATA3	chr13:39259974-39260777	MCF-7	breast:	n/a	n/a
37	CTBP2	chr13:39260245-39262457	H1-hESC	embryonic stem cell:	n/a	n/a
38	FOXM1	chr13:39259936-39260785	MCF-7	breast:	n/a	n/a
39	MAX	chr13:39260425-39262136	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796
40	GATA3	chr13:39259943-39260931	MCF-7	breast:	n/a	chr13:39259962-39259972
41	HA-E2F1	chr13:39260257-39261857	MCF-7	breast:	n/a	chr13:39260302-39260316 chr13:39261047-39261061
42	MAX	chr13:39260631-39262256	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796
43	NR2F2	chr13:39259984-39261082	MCF-7	breast:	n/a	n/a
44	KAP1	chr13:39259931-39261401	HEK293	kidney:	n/a	n/a
45	POLR2A	chr13:39260187-39261535	MCF-7	breast:	n/a	n/a
46	EP300	chr13:39260016-39260760	MCF-7	breast:	n/a	chr13:39260616-39260632
47	SIN3AK20	chr13:39260439-39260788	H1-hESC	embryonic stem cell:	n/a	n/a
48	HDAC2	chr13:39260145-39261505	MCF-7	breast:	n/a	chr13:39261248-39261267 chr13:39260513-39260527

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	chr13:39258919..39260831-chr13:39305195..39307479,2	MCF-7	breast:
6	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:
7	chr13:39259811..39260806-chr13:39337692..39338863,8	MCF-7	breast:
8	chr13:39255037..39256959-chr13:39258816..39261083,2	MCF-7	breast:

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

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11147723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11147724	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17244358	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2053848	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122208	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122212	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2197879	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442335	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442339	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442340	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442341	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442343	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442344	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2442373	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442379	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496418	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496419	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496425	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2496430	0.85[AMR][1000 genomes]
rs2496433	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35378642	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4329795	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55860060	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55880170	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs55922882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563629	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331440	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7991701	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs895895	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs930659	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs930660	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9566354	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9576589	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576590	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576591	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576592	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576595	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634754	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9788341	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][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
rs11147725	CSNK1A1L	cis	cerebellum	SCAN
rs11147725	CCNA1	cis	parietal	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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