Variant report

Variant	rs12059398
Chromosome Location	chr1:175041573-175041574
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175041206..175043201-chr1:175056003..175057829,2	K562	blood:
2	chr1:175041397..175042225-chr14:23298848..23299502,2	NB4	blood:

Variant related genes	Relation type
ENSG00000155465	Chromatin interaction
ENSG00000172590	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11577778	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11578942	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11578961	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11582121	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11583313	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12065394	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068402	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068982	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12076122	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16847779	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17302688	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17374668	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269647	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55808408	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55967803	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56226643	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59822966	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61541139	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6665471	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695255	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6703193	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9650986	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011472	chr1:175013165-175042885	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1012861	chr1:175021780-175063160	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv535210	chr1:175021780-175063160	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv825487	chr1:175031609-175113572	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175039800-175042400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:175039800-175046600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:175040200-175041800	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:175040400-175042800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:175040400-175043200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:175040600-175044000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:175040800-175042000	Enhancers	Fetal Lung	lung
8	chr1:175040800-175043000	Enhancers	Fetal Stomach	stomach
9	chr1:175041000-175041600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:175041000-175042000	Enhancers	Lung	lung
11	chr1:175041000-175042200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:175041000-175042400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:175041000-175042400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:175041000-175042600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr1:175041000-175043000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:175041000-175043000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:175041000-175043400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:175041000-175044000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:175041000-175044200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:175041000-175044200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:175041200-175041600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr1:175041200-175041600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr1:175041200-175041600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr1:175041200-175041600	Enhancers	Colonic Mucosa	Colon
25	chr1:175041200-175041600	Flanking Active TSS	Fetal Brain Male	brain
26	chr1:175041200-175041800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:175041200-175041800	Active TSS	Brain Germinal Matrix	brain
28	chr1:175041200-175041800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:175041200-175041800	Enhancers	Psoas Muscle	Psoas
30	chr1:175041200-175041800	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr1:175041200-175042000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:175041200-175042000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:175041200-175042000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:175041200-175042000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:175041200-175042000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr1:175041200-175042000	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr1:175041200-175042200	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr1:175041200-175042200	Enhancers	Fetal Thymus	thymus
39	chr1:175041200-175042400	Enhancers	Placenta	Placenta
40	chr1:175041200-175042400	Enhancers	Spleen	Spleen
41	chr1:175041200-175042400	Flanking Active TSS	Dnd41	blood
42	chr1:175041200-175043200	Enhancers	H9 Cell Line	embryonic stem cell
43	chr1:175041400-175041600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
44	chr1:175041400-175041600	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr1:175041400-175041600	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr1:175041400-175041600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:175041400-175041600	Active TSS	Fetal Brain Female	brain
48	chr1:175041400-175041600	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr1:175041400-175041600	Flanking Active TSS	HSMMtube	muscle
50	chr1:175041400-175041800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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