Variant report

Variant	rs12469873
Chromosome Location	chr2:58398340-58398341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11125745	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11889211	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12475594	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17049378	0.90[EUR][1000 genomes]
rs17049429	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2192690	0.91[AMR][1000 genomes]
rs4395240	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56705143	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56730649	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6725148	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6732505	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6735296	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72810360	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72810373	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72812357	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7594702	0.91[EUR][1000 genomes];0.87[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	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:58368600-58399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:58380800-58398800	Weak transcription	Spleen	Spleen
12	chr2:58381000-58398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
14	chr2:58382600-58400400	Weak transcription	Gastric	stomach
15	chr2:58382800-58398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:58382800-58398800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:58382800-58399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:58383200-58398800	Weak transcription	Esophagus	oesophagus
20	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
22	chr2:58385200-58424600	Weak transcription	Ovary	ovary
23	chr2:58385400-58400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:58388800-58401800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:58389000-58423200	Weak transcription	NHLF	lung
27	chr2:58389600-58431000	Weak transcription	HUVEC	blood vessel
28	chr2:58389800-58421000	Weak transcription	K562	blood
29	chr2:58390000-58399000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:58390200-58421200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:58390400-58400800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:58390600-58398800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:58391000-58467000	Weak transcription	HMEC	breast
34	chr2:58392200-58398800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:58392200-58414200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:58392600-58408200	Weak transcription	A549	lung
37	chr2:58392600-58415600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:58393000-58404000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:58394000-58414800	Weak transcription	Hela-S3	cervix
40	chr2:58394600-58407800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:58394800-58405000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:58395600-58400400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:58396000-58399600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:58396400-58398800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:58396400-58398800	Weak transcription	Fetal Intestine Small	intestine
46	chr2:58396400-58398800	Weak transcription	Lung	lung
47	chr2:58396400-58399000	Weak transcription	Aorta	Aorta
48	chr2:58396400-58399000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:58396400-58399200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:58396400-58438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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