Variant report

Variant	rs3759080
Chromosome Location	chr12:45611602-45611603
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	MXI1	chr12:45608368-45612550	SK-N-SH	brain:	n/a	n/a
2	CHD1	chr12:45608396-45612092	IMR90	lung:	n/a	chr12:45610369-45610379
3	RAD21	chr12:45608490-45611729	SK-N-SH	brain:	n/a	chr12:45610730-45610743 chr12:45609157-45609164 chr12:45610550-45610560
4	RAD21	chr12:45608521-45611962	IMR90	lung:	n/a	chr12:45610730-45610743 chr12:45609157-45609164 chr12:45610550-45610560
5	FOXA1	chr12:45611397-45611880	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:45608631-45612002	IMR90	lung:	n/a	n/a
7	RCOR1	chr12:45608678-45611872	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:45611560-45611624	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:45611598-45611802	ProgFib	skin:	n/a	n/a
10	BRCA1	chr12:45610444-45611707	Hela-S3	cervix:	n/a	n/a
11	FOXA2	chr12:45611593-45611884	HepG2	liver:	n/a	n/a
12	FOXA1	chr12:45611378-45611974	HepG2	liver:	n/a	n/a
13	FOXA1	chr12:45611586-45611883	HepG2	liver:	n/a	n/a
14	FOXA1	chr12:45611555-45611843	T-47D	breast:	n/a	n/a
15	STAT3	chr12:45611596-45611730	MCF10A-Er-Src	breast:	n/a	n/a
16	FOXA1	chr12:45611428-45611888	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:45611569..45613822-chr12:45799872..45802476,2	MCF-7	breast:
2	chr12:45593253..45599943-chr12:45607385..45612735,9	MCF-7	breast:
3	chr12:45610131..45611639-chr12:45621974..45623709,2	MCF-7	breast:
4	chr12:45600941..45603033-chr12:45611069..45612571,2	K562	blood:

Variant related genes	Relation type
PLEKHA8P1	TF binding region
ENSG00000257738	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1015626	0.81[AMR][1000 genomes]
rs10437984	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10459293	0.91[EUR][1000 genomes]
rs10459294	0.91[EUR][1000 genomes]
rs10492284	0.91[EUR][1000 genomes]
rs10748412	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10785556	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10785557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785566	0.81[AMR][1000 genomes]
rs10880755	0.86[AMR][1000 genomes]
rs10880756	0.86[AMR][1000 genomes]
rs10880760	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880761	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880762	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880763	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880764	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880771	0.81[AMR][1000 genomes]
rs11182903	0.81[EUR][1000 genomes]
rs11182904	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11182905	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182908	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11182912	0.89[EUR][1000 genomes]
rs11182913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182916	0.91[EUR][1000 genomes]
rs11182917	0.91[EUR][1000 genomes]
rs11182918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182919	0.91[EUR][1000 genomes]
rs11182921	0.91[EUR][1000 genomes]
rs11182922	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11182923	0.91[EUR][1000 genomes]
rs11182927	0.91[EUR][1000 genomes]
rs11182931	0.91[EUR][1000 genomes]
rs11182935	0.91[EUR][1000 genomes]
rs11182936	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11182938	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11182939	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11182940	0.91[EUR][1000 genomes]
rs11182941	0.91[EUR][1000 genomes]
rs11182942	0.81[EUR][1000 genomes]
rs11182943	0.91[EUR][1000 genomes]
rs11182944	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182946	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182947	0.89[EUR][1000 genomes]
rs11182949	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11561532	0.91[EUR][1000 genomes]
rs11610233	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11611509	0.81[EUR][1000 genomes]
rs11612203	0.91[EUR][1000 genomes]
rs11612233	0.91[EUR][1000 genomes]
rs11615850	0.91[EUR][1000 genomes]
rs12226944	0.82[EUR][1000 genomes]
rs12227678	0.91[EUR][1000 genomes]
rs12228733	0.81[EUR][1000 genomes]
rs12230322	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12231753	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12299174	0.81[EUR][1000 genomes]
rs12320168	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12320437	0.89[EUR][1000 genomes]
rs12322087	0.81[EUR][1000 genomes]
rs12814332	0.89[EUR][1000 genomes]
rs12815115	0.91[EUR][1000 genomes]
rs12815577	0.91[ASN][1000 genomes]
rs12822746	0.91[EUR][1000 genomes]
rs12828052	0.85[EUR][1000 genomes]
rs1399721	0.81[AMR][1000 genomes]
rs17095551	0.91[EUR][1000 genomes]
rs17095557	0.91[EUR][1000 genomes]
rs2052602	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2052603	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408184	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408185	0.91[EUR][1000 genomes]
rs34024171	0.91[EUR][1000 genomes]
rs35054776	0.91[EUR][1000 genomes]
rs35588430	0.81[EUR][1000 genomes]
rs35660715	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759077	0.91[EUR][1000 genomes]
rs3759081	0.91[EUR][1000 genomes]
rs3759082	0.87[EUR][1000 genomes]
rs3782131	0.91[EUR][1000 genomes]
rs4768085	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57797434	0.91[EUR][1000 genomes]
rs58444879	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61923810	0.91[EUR][1000 genomes]
rs61923825	0.91[EUR][1000 genomes]
rs61923830	0.91[EUR][1000 genomes]
rs7135988	0.81[AMR][1000 genomes]
rs7136368	0.81[AMR][1000 genomes]
rs7138983	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728590	0.81[AMR][1000 genomes]
rs7304481	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7309615	0.81[AMR][1000 genomes]
rs7956033	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7963038	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963057	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7964635	0.83[ASN][1000 genomes]
rs7971900	0.80[AMR][1000 genomes]
rs929903	0.81[AMR][1000 genomes]
rs9739519	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45608000-45611800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr12:45608200-45611800	Active TSS	HMEC	breast
3	chr12:45608200-45612400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr12:45608400-45611800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:45608400-45611800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:45608400-45611800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:45608400-45611800	Active TSS	NHDF-Ad	bronchial
8	chr12:45608400-45612200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr12:45608400-45612400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:45608400-45613400	Active TSS	Stomach Smooth Muscle	stomach
11	chr12:45608600-45611800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr12:45608600-45611800	Active TSS	Placenta	Placenta
13	chr12:45608600-45611800	Active TSS	Left Ventricle	heart
14	chr12:45608600-45611800	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr12:45608600-45611800	Active TSS	HSMM	muscle
16	chr12:45608600-45611800	Active TSS	HSMMtube	muscle
17	chr12:45608600-45612000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:45608600-45612000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:45608600-45612000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:45608600-45612000	Active TSS	Fetal Intestine Small	intestine
21	chr12:45608600-45612000	Active TSS	Fetal Muscle Leg	muscle
22	chr12:45608600-45612200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr12:45608600-45612200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:45608600-45612200	Active TSS	Colon Smooth Muscle	Colon
25	chr12:45608600-45612200	Active TSS	Placenta Amnion	Placenta Amnion
26	chr12:45608600-45612200	Active TSS	Psoas Muscle	Psoas
27	chr12:45608600-45612200	Active TSS	Right Ventricle	heart
28	chr12:45608600-45612400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:45608600-45612400	Active TSS	Fetal Intestine Large	intestine
30	chr12:45608600-45612400	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr12:45608600-45612400	Active TSS	NHLF	lung
32	chr12:45608600-45612800	Active TSS	Ovary	ovary
33	chr12:45608800-45611800	Active TSS	Brain Angular Gyrus	brain
34	chr12:45608800-45611800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:45608800-45612000	Active TSS	Rectal Smooth Muscle	rectum
36	chr12:45608800-45612200	Active TSS	Fetal Thymus	thymus
37	chr12:45608800-45612200	Active TSS	GM12878-XiMat	blood
38	chr12:45608800-45612800	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr12:45608800-45613400	Active TSS	Aorta	Aorta
40	chr12:45609000-45611800	Active TSS	HUVEC	blood vessel
41	chr12:45609000-45611800	Active TSS	NH-A	brain
42	chr12:45609000-45611800	Active TSS	Osteobl	bone
43	chr12:45610200-45612200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr12:45610400-45612000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:45610400-45612600	Active TSS	Right Atrium	heart
46	chr12:45610600-45612000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr12:45610600-45612200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:45610600-45612400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:45610800-45611800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr12:45610800-45611800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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