Variant report

Variant	rs59475580
Chromosome Location	chr1:57035775-57035776
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	chr1:57007850..57009475-chr1:57034148..57036115,2	MCF-7	breast:
2	chr1:57034051..57037170-chr1:57042979..57045749,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162407	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10888981	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418521	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17114110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17114113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17114115	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17114126	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114127	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114133	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55927525	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58146416	0.89[EUR][1000 genomes]
rs72664369	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72664370	0.89[EUR][1000 genomes]
rs72664380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664392	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664395	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72666448	0.89[EUR][1000 genomes]
rs72666498	0.89[EUR][1000 genomes]
rs72668306	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57016000-57038600	Weak transcription	HSMMtube	muscle
2	chr1:57017400-57039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:57017800-57040800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:57025600-57040000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:57029400-57042200	Weak transcription	Thymus	Thymus
6	chr1:57030800-57036800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:57032000-57036800	Weak transcription	Fetal Stomach	stomach
8	chr1:57032000-57038800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:57032200-57038000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:57032200-57040600	Weak transcription	HSMM	muscle
11	chr1:57032400-57042400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:57032600-57036800	Weak transcription	Fetal Heart	heart
13	chr1:57032800-57036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:57032800-57037600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:57032800-57038200	Weak transcription	Osteobl	bone
16	chr1:57032800-57039200	Weak transcription	Small Intestine	intestine
17	chr1:57032800-57041000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:57033000-57036600	Weak transcription	Fetal Kidney	kidney
19	chr1:57033000-57036800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:57033000-57038200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:57033000-57038800	Weak transcription	Fetal Brain Male	brain
22	chr1:57033800-57036600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:57033800-57039800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:57034200-57035800	Enhancers	Left Ventricle	heart
25	chr1:57034200-57035800	Enhancers	Psoas Muscle	Psoas
26	chr1:57034200-57036800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:57034200-57038200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:57034400-57035800	Enhancers	Lung	lung
29	chr1:57034400-57036600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:57034400-57036800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:57034600-57035800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:57034600-57035800	Enhancers	Pancreas	Pancrea
33	chr1:57035000-57035800	Enhancers	Placenta	Placenta
34	chr1:57035200-57035800	Enhancers	Duodenum Mucosa	Duodenum
35	chr1:57035200-57036800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:57035200-57036800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:57035200-57037800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr1:57035200-57039600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:57035200-57039600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:57035200-57039600	Enhancers	Fetal Intestine Large	intestine
41	chr1:57035200-57041400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:57035400-57035800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:57035400-57035800	Enhancers	H9 Cell Line	embryonic stem cell
44	chr1:57035400-57035800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:57035400-57035800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:57035400-57035800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:57035400-57035800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:57035400-57035800	Enhancers	Aorta	Aorta
49	chr1:57035400-57035800	Enhancers	Brain Anterior Caudate	brain
50	chr1:57035400-57035800	Enhancers	Brain Hippocampus Middle	brain

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