Variant report

Variant	rs12078260
Chromosome Location	chr1:57109814-57109815
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	MAZ	chr1:57109756-57111909	IMR90	lung:	n/a	n/a
2	FOXA2	chr1:57109189-57110009	HepG2	liver:	n/a	n/a
3	TBP	chr1:57109814-57110582	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:57109759-57112147	Hela-S3	cervix:	n/a	n/a
5	ARID3A	chr1:57109126-57110185	HepG2	liver:	n/a	n/a
6	GATA2	chr1:57109506-57110121	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
PRKAA2	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10749708	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10789036	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789038	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10789040	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10789041	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10889006	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10889008	1.00[ASW][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10889009	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11206884	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11206885	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206886	0.91[ASN][1000 genomes]
rs11206888	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206889	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206890	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11206895	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1124900	0.83[AMR][1000 genomes]
rs11589368	0.85[ASN][1000 genomes]
rs11804779	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12021768	0.95[ASN][1000 genomes]
rs12021851	0.95[ASN][1000 genomes]
rs12023668	0.85[ASN][1000 genomes]
rs12032999	0.92[ASN][1000 genomes]
rs12046428	0.83[ASN][1000 genomes]
rs12048572	0.85[ASN][1000 genomes]
rs12073311	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12092267	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12097148	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12738355	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13374924	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1418442	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs1986660	0.95[ASN][1000 genomes]
rs2404718	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404992	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2404993	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2746345	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2746348	1.00[ASW][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap]
rs2746349	1.00[ASW][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap]
rs2746353	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796517	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2796519	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2796523	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2796527	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4548471	0.95[ASN][1000 genomes]
rs4551620	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4562656	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4584419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59223968	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61772962	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61774287	0.95[ASN][1000 genomes]
rs61774288	0.90[AFR][1000 genomes]
rs6588641	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6588643	0.81[AMR][1000 genomes]
rs72666470	0.90[ASN][1000 genomes]
rs7419053	0.92[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[ASN][1000 genomes]
rs7515414	0.92[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.83[ASN][1000 genomes]
rs7519509	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545066	0.83[ASN][1000 genomes]
rs7546264	0.85[ASN][1000 genomes]
rs7547486	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932447	0.92[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[ASN][1000 genomes]
rs9887834	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9887940	0.85[AMR][1000 genomes];0.85[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3371942	chr1:57109389-57112237	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57105600-57110000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:57105600-57110200	Weak transcription	HSMMtube	muscle
3	chr1:57109200-57110000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:57109200-57110000	Enhancers	Fetal Intestine Small	intestine
5	chr1:57109400-57110000	Enhancers	Liver	Liver
6	chr1:57109400-57110000	Enhancers	NHDF-Ad	bronchial
7	chr1:57109600-57110200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:57109800-57110000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
9	chr1:57109800-57110000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:57109800-57110000	Bivalent Enhancer	Primary T cells from cord blood	blood
11	chr1:57109800-57110000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:57109800-57110000	Enhancers	Colon Smooth Muscle	Colon
13	chr1:57109800-57110000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:57109800-57110000	Flanking Active TSS	Fetal Intestine Large	intestine
15	chr1:57109800-57110000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr1:57109800-57110000	Flanking Active TSS	Fetal Lung	lung
17	chr1:57109800-57110000	Enhancers	Ovary	ovary
18	chr1:57109800-57110000	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:57109800-57110000	Flanking Active TSS	Hela-S3	cervix
20	chr1:57109800-57110000	Enhancers	NHLF	lung
21	chr1:57109800-57110200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
22	chr1:57109800-57110200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:57109800-57110200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr1:57109800-57110200	Flanking Active TSS	Fetal Brain Male	brain
25	chr1:57109800-57110200	Flanking Active TSS	Fetal Heart	heart
26	chr1:57109800-57110200	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
27	chr1:57109800-57110200	Active TSS	Fetal Muscle Trunk	muscle
28	chr1:57109800-57110200	Flanking Active TSS	Fetal Stomach	stomach
29	chr1:57109800-57110200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:57109800-57110200	Flanking Active TSS	A549	lung
31	chr1:57109800-57110200	Flanking Active TSS	HepG2	liver
32	chr1:57109800-57110400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:57109800-57110400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr1:57109800-57110600	Flanking Active TSS	HUVEC	blood vessel
35	chr1:57109800-57110800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:57109800-57111000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:57109800-57111200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:57109800-57111400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
39	chr1:57109800-57111600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:57109800-57111600	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr1:57109800-57111800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
42	chr1:57109800-57112000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr1:57109800-57112000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr1:57109800-57112000	Active TSS	Psoas Muscle	Psoas
45	chr1:57109800-57112200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr1:57109800-57112200	Active TSS	Brain Angular Gyrus	brain
47	chr1:57109800-57112400	Active TSS	Rectal Smooth Muscle	rectum
48	chr1:57109800-57113200	Active TSS	Right Atrium	heart
49	chr1:57109800-57114600	Active TSS	Skeletal Muscle Female	skeletal muscle

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