Variant report

Variant	rs62577464
Chromosome Location	chr9:104500627-104500628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10512288	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10819985	0.89[AFR][1000 genomes]
rs10989610	0.86[AFR][1000 genomes]
rs16920674	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2069324	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743485	0.89[AFR][1000 genomes]
rs55665802	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55682946	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55971755	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56236943	0.99[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59275233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576354	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62576359	0.82[EUR][1000 genomes]
rs62577460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62577463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62577465	0.89[EUR][1000 genomes]
rs62582206	0.89[EUR][1000 genomes]
rs6479062	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6479064	0.94[AFR][1000 genomes]
rs7020326	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7030816	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7031850	0.82[EUR][1000 genomes]
rs7032033	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7033120	0.83[AFR][1000 genomes]
rs7034155	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7041051	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7043125	0.82[EUR][1000 genomes]
rs7043519	0.82[EUR][1000 genomes]
rs7849732	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7849944	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7853624	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7864316	0.81[AFR][1000 genomes]
rs7864726	0.99[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
3	nsv1046590	chr9:104450624-104848588	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1046614	chr9:104492314-104686326	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1054992	chr9:104494816-104771134	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1043967	chr9:104498664-104636328	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104497800-104501200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:104499000-104501200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
3	chr9:104499200-104501000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
4	chr9:104499200-104501000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
5	chr9:104499400-104501000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr9:104499400-104501600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr9:104499600-104501000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr9:104499600-104501000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
9	chr9:104499600-104501200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr9:104499600-104501200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:104499600-104501200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
12	chr9:104499600-104501200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
13	chr9:104499600-104501400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:104499800-104501000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:104499800-104501200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr9:104499800-104501200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
17	chr9:104499800-104501200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
18	chr9:104499800-104501200	Active TSS	Right Atrium	heart
19	chr9:104500000-104500800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
20	chr9:104500000-104501000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
21	chr9:104500000-104501000	Flanking Active TSS	Pancreas	Pancrea
22	chr9:104500000-104501000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
23	chr9:104500000-104501200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr9:104500000-104501200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:104500000-104501600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr9:104500200-104500800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:104500200-104500800	Bivalent Enhancer	HMEC	breast
28	chr9:104500200-104501000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:104500200-104501000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:104500200-104501000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr9:104500200-104501000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:104500200-104501000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
33	chr9:104500200-104501000	Active TSS	Brain Substantia Nigra	brain
34	chr9:104500200-104501000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
35	chr9:104500200-104501000	Bivalent Enhancer	Placenta	Placenta
36	chr9:104500200-104501000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
37	chr9:104500200-104501000	Bivalent/Poised TSS	A549	lung
38	chr9:104500200-104501200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr9:104500200-104501200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:104500200-104501200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:104500200-104501200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:104500200-104501200	Flanking Active TSS	Liver	Liver
43	chr9:104500200-104501200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
44	chr9:104500200-104501200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr9:104500200-104501200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr9:104500200-104501200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
47	chr9:104500200-104501200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
48	chr9:104500200-104501400	Active TSS	Ovary	ovary
49	chr9:104500400-104500800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:104500400-104500800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood

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