Variant report

Variant	rs12090072
Chromosome Location	chr1:59399934-59399935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59392641..59396388-chr1:59399124..59401431,3	K562	blood:
2	chr1:59388758..59390537-chr1:59398556..59401033,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10158831	0.80[EUR][1000 genomes]
rs10889121	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207331	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2038863	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477745	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716113	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2716115	0.91[EUR][1000 genomes]
rs2716127	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764911	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2764914	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2764915	0.87[EUR][1000 genomes]
rs2764917	0.87[EUR][1000 genomes]
rs2953376	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015312	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4528141	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59389000-59407000	Weak transcription	Spleen	Spleen
2	chr1:59389200-59401400	Weak transcription	Left Ventricle	heart
3	chr1:59393600-59400800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:59393600-59406800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:59395800-59400000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:59396000-59400400	Enhancers	Hela-S3	cervix
7	chr1:59398800-59400400	Enhancers	Stomach Mucosa	stomach
8	chr1:59398800-59402000	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr1:59398800-59403000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:59399000-59405800	Weak transcription	Pancreas	Pancrea
11	chr1:59399000-59406800	Weak transcription	Esophagus	oesophagus
12	chr1:59399000-59407000	Weak transcription	Lung	lung
13	chr1:59399200-59400400	Weak transcription	Fetal Stomach	stomach
14	chr1:59399200-59400800	Enhancers	NHEK	skin
15	chr1:59399200-59407200	Weak transcription	Colonic Mucosa	Colon
16	chr1:59399200-59409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:59399400-59401400	Weak transcription	Gastric	stomach
18	chr1:59399400-59402200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:59399400-59405200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:59399400-59405800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:59399600-59401200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:59399600-59401200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:59399600-59402400	Weak transcription	A549	lung
24	chr1:59399600-59402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:59399800-59401200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:59399800-59402600	Weak transcription	HMEC	breast

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