Variant report

Variant	rs1044826
Chromosome Location	chr3:139073011-139073012
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	CTCF	chr3:139072781-139073123	ECC-1	luminal epithelium:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
2	CTCF	chr3:139072694-139073237	T-47D	breast:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
3	CTCF	chr3:139072862-139073087	Kidney_OC	kidney:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
4	CTCF	chr3:139072881-139073072	GM19239	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
5	CTCF	chr3:139072900-139073050	HCT-116	colon:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
6	ZNF143	chr3:139072832-139073116	GM12878	blood:	n/a	n/a
7	FOS	chr3:139072735-139073111	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr3:139072900-139073050	HAc	cerebellar:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
9	CTCF	chr3:139072814-139073118	ECC-1	luminal epithelium:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
10	POLR2A	chr3:139072709-139073185	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr3:139069653-139075359	GM12878	blood:	n/a	n/a
12	CTCF	chr3:139072689-139073205	HepG2	liver:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
13	MYC	chr3:139072844-139073095	K562	blood:	n/a	n/a
14	ARID3A	chr3:139072609-139073255	K562	blood:	n/a	n/a
15	STAT3	chr3:139072581-139073380	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr3:139072880-139073030	AoAF	blood vessel:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
17	CTCF	chr3:139072889-139073061	MCF-7	breast:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
18	CTCF	chr3:139072920-139073070	HPAF	blood vessel:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
19	CTCF	chr3:139072900-139073050	Caco-2	colon:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
20	ZNF143	chr3:139072817-139073143	H1-hESC	embryonic stem cell:	n/a	n/a
21	RUNX3	chr3:139072816-139073132	GM12878	blood:	n/a	chr3:139072972-139072987
22	CTCF	chr3:139072869-139073094	GM10248	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
23	CTCF	chr3:139072900-139073050	GM12871	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
24	CTCF	chr3:139072940-139073090	GM12864	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
25	CTCF	chr3:139072874-139073089	GM13977	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
26	CTCF	chr3:139072809-139073120	HepG2	liver:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
27	CTCF	chr3:139072870-139073083	NHEK	skin:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
28	CTCF	chr3:139072844-139073108	MCF-7	breast:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
29	CTCF	chr3:139072920-139073070	NHEK	skin:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
30	CTCF	chr3:139072920-139073070	RPTEC	kidney:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
31	POLR2A	chr3:139072850-139073070	HCT-116	colon:	n/a	n/a
32	CTCF	chr3:139072920-139073070	HEK293	kidney:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
33	CTCF	chr3:139072880-139073030	HCT-116	colon:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
34	CTCF	chr3:139072880-139073030	HCPEpiC	choroid plexus:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
35	RAD21	chr3:139072882-139073094	K562	blood:	n/a	n/a
36	CTCF	chr3:139072880-139073030	GM12864	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
37	CTCF	chr3:139072891-139073077	GM13976	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
38	CTCF	chr3:139072920-139073070	AG09319	gingival:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
39	CTCF	chr3:139072746-139073253	A549	lung:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
40	CTCF	chr3:139072718-139073383	K562	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
41	CTCF	chr3:139072900-139073050	HVMF	connective:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
42	RAD21	chr3:139072775-139073239	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr3:139070258-139074075	U87	brain:	n/a	n/a
44	CTCF	chr3:139072920-139073070	NB4	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
45	CTCF	chr3:139072697-139073237	K562	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
46	CTCF	chr3:139072920-139073070	SAEC	small airway:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
47	RAD21	chr3:139072845-139073094	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr3:139072900-139073050	HepG2	liver:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
49	USF2	chr3:139072811-139073174	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr3:139072826-139073127	K562	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008

No.	Distal block	Cell Line	Cell type
1	chr3:139072256..139074431-chr3:139078607..139080931,2	MCF-7	breast:
2	chr3:139072544..139073416-chr3:139280346..139281512,5	MCF-7	breast:
3	chr3:139047930..139048680-chr3:139072548..139073494,2	K562	blood:
4	chr3:139072091..139074896-chr3:139076494..139078712,3	K562	blood:
5	chr3:138847869..138848524-chr3:139072496..139073303,2	K562	blood:
6	chr3:138830352..138831184-chr3:139072519..139073327,2	MCF-7	breast:
7	chr3:139072193..139074257-chr3:139106179..139110026,3	MCF-7	breast:
8	chr3:139072517..139075084-chr3:139096841..139099787,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272656	TF binding region
ENSG00000248932	Chromatin interaction
ENSG00000252245	Chromatin interaction
ENSG00000184432	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10460845	0.83[ASN][1000 genomes]
rs1080371	0.83[CHD][hapmap]
rs10935320	0.97[ASN][1000 genomes]
rs10935323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11706615	0.81[YRI][hapmap]
rs12488939	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12494806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12695698	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12695699	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12695700	0.83[AMR][1000 genomes]
rs13060697	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13074208	0.81[AMR][1000 genomes]
rs13083195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085888	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13086868	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13089007	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13089090	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13092507	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13092935	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1586861	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1586863	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1586864	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs167187	0.83[CHD][hapmap]
rs17336869	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs188421	0.83[CHD][hapmap]
rs1907687	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2233811	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2233815	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2349059	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34623690	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772877	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3772878	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3772879	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3821544	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821545	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4544576	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683464	0.83[CHD][hapmap]
rs6439860	0.83[CHD][hapmap]
rs6771831	0.83[CHD][hapmap]
rs67929453	0.92[ASN][1000 genomes]
rs7374385	0.83[EUR][1000 genomes]
rs9289576	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9289578	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs964227	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs973691	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9812192	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9818691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9825064	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9831108	0.90[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834607	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9835241	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9848241	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9849039	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9849578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9853350	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9859864	0.83[CHD][hapmap]
rs9860201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860521	0.83[AMR][1000 genomes]
rs9868544	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9882014	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1044826	BPESC1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139064000-139073400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:139064000-139073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:139064000-139073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
6	chr3:139064800-139074800	Weak transcription	Right Atrium	heart
7	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
8	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
9	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
10	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:139065000-139103800	Strong transcription	HSMM	muscle
12	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:139065200-139073200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:139065200-139073200	Strong transcription	K562	blood
15	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:139065400-139073800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:139065400-139077000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:139065400-139077600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:139065400-139097600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:139065400-139102600	Strong transcription	Osteobl	bone
29	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
31	chr3:139065600-139073200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:139065600-139077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:139065600-139079600	Strong transcription	Fetal Lung	lung
34	chr3:139065600-139100200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:139065600-139101800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:139065600-139102400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:139065600-139102400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:139065600-139102400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:139065600-139103600	Strong transcription	HUVEC	blood vessel
40	chr3:139065600-139103600	Strong transcription	NH-A	brain
41	chr3:139065600-139103800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:139065600-139103800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:139065800-139074200	Strong transcription	Adipose Nuclei	Adipose
44	chr3:139065800-139078000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:139065800-139080800	Strong transcription	Brain Germinal Matrix	brain
46	chr3:139065800-139081000	Strong transcription	Fetal Brain Female	brain
47	chr3:139065800-139095000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:139065800-139096200	Strong transcription	Liver	Liver
49	chr3:139065800-139098200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:139065800-139098200	Strong transcription	HMEC	breast

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