Variant report

Variant	rs12024405
Chromosome Location	chr1:85796245-85796246
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12022538	0.85[ASN][1000 genomes]
rs12023006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024508	0.85[ASN][1000 genomes]
rs12029474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029684	0.94[ASN][1000 genomes]
rs12033170	0.89[ASN][1000 genomes]
rs12033473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034206	0.94[ASN][1000 genomes]
rs12034481	0.94[ASN][1000 genomes]
rs12036146	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038279	0.90[ASN][1000 genomes]
rs12039188	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041140	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043505	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043604	0.85[ASN][1000 genomes]
rs12045545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046433	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047139	0.81[ASN][1000 genomes]
rs12047220	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12049582	0.85[ASN][1000 genomes]
rs2300638	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28847138	0.98[ASN][1000 genomes]
rs3813603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58489234	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85788600-85797400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:85790400-85797000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:85790600-85800000	Enhancers	HUVEC	blood vessel
4	chr1:85791000-85796800	Enhancers	HepG2	liver
5	chr1:85791200-85798000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:85791400-85797400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:85792200-85796400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:85792200-85806000	Weak transcription	Fetal Kidney	kidney
9	chr1:85792600-85797800	Weak transcription	Fetal Intestine Small	intestine
10	chr1:85792800-85796600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:85793000-85797000	Enhancers	HMEC	breast
12	chr1:85793200-85797000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:85793200-85797600	Enhancers	NHEK	skin
14	chr1:85793200-85798600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:85793400-85797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:85793600-85798200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:85794000-85796600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr1:85794000-85797000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:85794000-85798200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:85794200-85796600	Enhancers	Placenta	Placenta
21	chr1:85794200-85798000	Enhancers	Fetal Muscle Leg	muscle
22	chr1:85794400-85796800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:85794400-85797400	Enhancers	Fetal Heart	heart
24	chr1:85794600-85796600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:85794600-85796800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:85794600-85797600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:85794800-85796400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:85794800-85798200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr1:85795000-85796400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:85795000-85796600	Enhancers	Brain Hippocampus Middle	brain
31	chr1:85795000-85796800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:85795000-85798000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:85795200-85796400	Enhancers	A549	lung
34	chr1:85795200-85798600	Weak transcription	Fetal Intestine Large	intestine
35	chr1:85795400-85796600	Enhancers	Stomach Mucosa	stomach
36	chr1:85795400-85797000	Enhancers	Placenta Amnion	Placenta Amnion
37	chr1:85795600-85796400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:85795600-85796600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr1:85795600-85796600	Enhancers	H9 Cell Line	embryonic stem cell
40	chr1:85795600-85796600	Flanking Active TSS	HSMMtube	muscle
41	chr1:85795600-85796600	Flanking Active TSS	NH-A	brain
42	chr1:85795600-85796800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:85795600-85796800	Enhancers	Left Ventricle	heart
44	chr1:85795600-85796800	Enhancers	Right Ventricle	heart
45	chr1:85795600-85796800	Enhancers	Spleen	Spleen
46	chr1:85795600-85796800	Flanking Active TSS	NHDF-Ad	bronchial
47	chr1:85795600-85797000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:85795600-85797000	Enhancers	Brain Germinal Matrix	brain
49	chr1:85795600-85797000	Enhancers	Right Atrium	heart
50	chr1:85795600-85798400	Enhancers	Primary B cells from peripheral blood	blood

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