Variant report

Variant	rs12404858
Chromosome Location	chr1:62167108-62167109
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:62166879..62169010-chr1:62188988..62191312,3	K562	blood:
2	chr1:62165390..62168379-chr1:62189812..62192144,2	K562	blood:
3	chr1:62162809..62165053-chr1:62166918..62169427,2	K562	blood:
4	chr1:62164919..62167340-chr1:62169728..62172685,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162604	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11207811	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12026380	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12031230	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122681	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6675491	0.86[EUR][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	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 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	chr1:62136800-62173800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
3	chr1:62140000-62189000	Weak transcription	NHLF	lung
4	chr1:62142800-62172200	Weak transcription	Ovary	ovary
5	chr1:62142800-62188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:62143800-62170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:62145000-62172200	Weak transcription	Colonic Mucosa	Colon
8	chr1:62145200-62167400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:62146200-62190200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:62147600-62173400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:62152400-62175200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:62154800-62171600	Weak transcription	Fetal Heart	heart
13	chr1:62155400-62167400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:62155400-62167800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:62155400-62167800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:62155400-62169000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:62158600-62189800	Weak transcription	Pancreas	Pancrea
18	chr1:62159200-62167400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:62159200-62167600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:62159200-62167600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:62159200-62167600	Strong transcription	Adipose Nuclei	Adipose
22	chr1:62159200-62167800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:62159400-62168600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:62160800-62167600	Strong transcription	HUVEC	blood vessel
25	chr1:62161200-62167400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:62161200-62167600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:62161200-62180600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:62161600-62167600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:62161600-62167800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:62161600-62168400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:62161800-62179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:62162200-62167400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:62162200-62167400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:62162200-62167800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:62162200-62167800	Strong transcription	Osteobl	bone
36	chr1:62162400-62167600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:62162400-62168000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:62162600-62167600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:62162600-62167600	Strong transcription	Dnd41	blood
40	chr1:62162600-62177400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:62162800-62167200	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:62162800-62167600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:62162800-62168600	Strong transcription	Primary B cells from cord blood	blood
44	chr1:62163000-62167600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:62163000-62167600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:62163000-62168000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:62163200-62167600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:62163200-62172800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:62163400-62167400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:62163400-62181800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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