Variant report

Variant	rs4533261
Chromosome Location	chr15:39722572-39722573
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	NR2F2	chr15:39722081-39722580	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:39721938-39723507	HUVEC	blood vessel:	n/a	n/a
3	RAD21	chr15:39722142-39722666	IMR90	lung:	n/a	n/a
4	GATA3	chr15:39722018-39722648	MCF-7	breast:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
5	PBX3	chr15:39722045-39722609	SK-N-SH	brain:	n/a	n/a
6	NR2F2	chr15:39722145-39722578	MCF-7	breast:	n/a	n/a
7	SPI1	chr15:39722021-39722616	GM12891	blood:	n/a	chr15:39722133-39722142 chr15:39722118-39722131
8	GATA3	chr15:39721977-39722657	SK-N-SH	brain:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
9	PBX3	chr15:39722023-39722632	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr15:39722017-39722695	MCF-7	breast:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
11	TCF12	chr15:39722003-39722666	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr15:39722052-39722606	A549	lung:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
13	GATA3	chr15:39721830-39722716	SK-N-SH	brain:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
14	JUN	chr15:39722036-39723003	HUVEC	blood vessel:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
15	EP300	chr15:39721999-39722791	SK-N-SH	brain:	n/a	chr15:39722128-39722142
16	SIN3AK20	chr15:39721925-39722757	MCF-7	breast:	n/a	n/a
17	NFIC	chr15:39721916-39722691	SK-N-SH	brain:	n/a	chr15:39722297-39722313
18	TCF12	chr15:39721924-39722750	SK-N-SH	brain:	n/a	n/a
19	JUND	chr15:39722021-39722670	SK-N-SH	brain:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
20	POLR2A	chr15:39722501-39722924	HUVEC	blood vessel:	n/a	n/a
21	RXRA	chr15:39722015-39722734	SK-N-SH	brain:	n/a	n/a
22	SPI1	chr15:39722563-39722894	HL-60	blood:	n/a	n/a
23	FOSL2	chr15:39721993-39722591	SK-N-SH	brain:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
24	EP300	chr15:39721978-39722672	SK-N-SH	brain:	n/a	chr15:39722128-39722142
25	MAX	chr15:39722199-39722589	SK-N-SH	brain:	n/a	n/a
26	EP300	chr15:39722036-39722577	MCF-7	breast:	n/a	chr15:39722128-39722142
27	POLR2A	chr15:39722190-39723527	HUVEC	blood vessel:	n/a	n/a
28	TCF12	chr15:39721965-39722647	A549	lung:	n/a	n/a
29	FOS	chr15:39722024-39722952	HUVEC	blood vessel:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
30	TEAD4	chr15:39722006-39722670	SK-N-SH	brain:	n/a	n/a
31	JUND	chr15:39722060-39722661	SK-N-SH	brain:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
32	POLR2A	chr15:39721760-39723490	HUVEC	blood vessel:	n/a	n/a
33	FOXM1	chr15:39722085-39722627	MCF-7	breast:	n/a	n/a
34	FOXA2	chr15:39722254-39722597	A549	lung:	n/a	n/a
35	POLR2A	chr15:39722098-39722572	SK-N-SH	brain:	n/a	n/a
36	IKZF1	chr15:39721948-39722638	GM12878	blood:	n/a	n/a
37	GATA2	chr15:39721959-39722959	HUVEC	blood vessel:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
38	SP1	chr15:39722080-39722635	A549	lung:	n/a	n/a
39	POLR2A	chr15:39722122-39723348	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr15:39721832-39723682	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:39721051..39725636-chr15:39870055..39875310,7	MCF-7	breast:
2	chr15:39722154..39722685-chr15:39960642..39961199,2	MCF-7	breast:
3	chr15:39721562..39724453-chr15:39734811..39737253,2	MCF-7	breast:
4	chr15:39720867..39723371-chr15:39870394..39874925,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259345	TF binding region
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11070204	0.81[YRI][hapmap]
rs11631986	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593294	0.83[YRI][hapmap]
rs12907034	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4244571	0.81[YRI][hapmap]
rs4462564	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4486853	0.82[AFR][1000 genomes]
rs4924350	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7182023	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8040081	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8040790	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9888722	0.83[YRI][hapmap]
rs9920130	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4533261	RP11-624L4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39712600-39724200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:39713200-39727400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:39719200-39723200	Enhancers	Left Ventricle	heart
4	chr15:39719200-39728200	Enhancers	HUVEC	blood vessel
5	chr15:39719400-39723400	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:39719400-39726800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:39719600-39723400	Enhancers	Fetal Thymus	thymus
8	chr15:39719600-39724200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:39719600-39725000	Weak transcription	Right Ventricle	heart
10	chr15:39719600-39727200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr15:39719800-39725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:39720000-39723800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr15:39720000-39724200	Enhancers	Thymus	Thymus
14	chr15:39720200-39723200	Enhancers	Primary T cells from cord blood	blood
15	chr15:39720200-39723800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:39720200-39723800	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:39720200-39723800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr15:39720200-39724000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:39720200-39725000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:39720200-39725000	Weak transcription	Fetal Stomach	stomach
21	chr15:39720200-39725600	Weak transcription	Lung	lung
22	chr15:39720200-39726800	Weak transcription	Adipose Nuclei	Adipose
23	chr15:39720400-39724000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:39720400-39726400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr15:39720800-39722600	Enhancers	Small Intestine	intestine
26	chr15:39721000-39724200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:39721200-39723000	Enhancers	Stomach Mucosa	stomach
28	chr15:39721400-39723200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:39721400-39724000	Enhancers	NH-A	brain
30	chr15:39721600-39722800	Enhancers	Fetal Intestine Large	intestine
31	chr15:39721600-39722800	Enhancers	Hela-S3	cervix
32	chr15:39721600-39724400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:39721600-39724600	Enhancers	Osteobl	bone
34	chr15:39721800-39722600	Enhancers	Primary B cells from cord blood	blood
35	chr15:39721800-39722600	Enhancers	Fetal Heart	heart
36	chr15:39721800-39722600	Flanking Active TSS	GM12878-XiMat	blood
37	chr15:39721800-39722600	Enhancers	K562	blood
38	chr15:39721800-39724400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:39721800-39725400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:39722000-39722600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr15:39722000-39722600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr15:39722000-39722800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:39722000-39722800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:39722000-39722800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:39722000-39722800	Enhancers	Spleen	Spleen
46	chr15:39722000-39722800	Enhancers	NHLF	lung
47	chr15:39722000-39723000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr15:39722000-39723000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr15:39722000-39723000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:39722000-39723000	Enhancers	HepG2	liver

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