Variant report

Variant	rs62578777
Chromosome Location	chr9:96929283-96929284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96885338..96887288-chr9:96929216..96930886,2	MCF-7	breast:
2	chr9:96927010..96929542-chr9:97400485..97402088,2	MCF-7	breast:
3	chr9:96337657..96339290-chr9:96927321..96930180,2	K562	blood:
4	chr9:96790341..96794271-chr9:96926817..96931236,5	K562	blood:
5	chr6:27860274..27861052-chr9:96928480..96929585,3	Hela-S3	cervix:
6	chr9:96773280..96775592-chr9:96928831..96930974,2	K562	blood:
7	chr9:96791956..96794354-chr9:96926207..96931491,6	MCF-7	breast:
8	chr12:53296484..53299330-chr9:96928573..96930295,2	MCF-7	breast:
9	chr14:90862960..90863497-chr9:96928700..96929562,2	Hela-S3	cervix:
10	chr10:75757238..75757954-chr9:96929118..96929804,2	Hela-S3	cervix:
11	chr1:201979347..201980302-chr9:96928844..96929674,2	Hela-S3	cervix:
12	chr9:96790823..96795467-chr9:96925835..96932235,7	K562	blood:
13	chr9:96845151..96850974-chr9:96927067..96931575,8	K562	blood:
14	chr1:113247853..113250339-chr9:96928983..96930846,2	K562	blood:
15	chr19:12901906..12902802-chr9:96928364..96929361,2	Hela-S3	cervix:
16	chr9:96927406..96930148-chr9:97007636..97010398,2	MCF-7	breast:
17	chr9:96792323..96794528-chr9:96927672..96930924,4	MCF-7	breast:
18	chr9:96212877..96215443-chr9:96928941..96930763,2	K562	blood:
19	chr6:136610448..136611121-chr9:96929034..96929855,2	Hela-S3	cervix:
20	chr9:96845151..96851769-chr9:96927067..96931565,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000163435	Chromatin interaction
ENSG00000252723	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000198668	Chromatin interaction
ENSG00000197724	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000234678	Chromatin interaction
ENSG00000158079	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000165140	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000029363	Chromatin interaction
ENSG00000035403	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10512231	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993068	0.96[ASN][1000 genomes]
rs10993069	0.96[ASN][1000 genomes]
rs10993090	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10993094	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11788788	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336926	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12337981	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338333	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338885	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12339587	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341175	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347752	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13295163	0.96[ASN][1000 genomes]
rs13439971	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13440059	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1421135	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34582118	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34765284	0.93[ASN][1000 genomes]
rs36044301	0.96[ASN][1000 genomes]
rs55881323	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56006511	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62575976	0.96[ASN][1000 genomes]
rs62575977	0.96[ASN][1000 genomes]
rs62578780	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62578801	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7037996	0.96[ASN][1000 genomes]
rs7041934	0.96[ASN][1000 genomes]
rs7864156	0.96[ASN][1000 genomes]
rs7868381	0.96[ASN][1000 genomes]
rs7871468	0.96[ASN][1000 genomes]
rs7873928	0.96[ASN][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	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking 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 miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3435412	chr9:96924949-96935312	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv3323629	chr9:96927556-96930104	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96927800-96929600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:96927800-96929600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr9:96927800-96929800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:96927800-96929800	Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr9:96927800-96929800	Active TSS	Brain Anterior Caudate	brain
6	chr9:96927800-96929800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr9:96927800-96929800	Active TSS	Lung	lung
8	chr9:96927800-96930000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:96927800-96930000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:96927800-96930000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:96927800-96930000	Active TSS	Osteobl	bone
12	chr9:96927800-96930200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr9:96927800-96930400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr9:96927800-96930400	Active TSS	Fetal Brain Female	brain
15	chr9:96927800-96930400	Active TSS	Stomach Smooth Muscle	stomach
16	chr9:96927800-96930800	Active TSS	Colonic Mucosa	Colon
17	chr9:96927800-96930800	Active TSS	NHLF	lung
18	chr9:96927800-96931000	Active TSS	Fetal Kidney	kidney
19	chr9:96927800-96931200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:96927800-96931400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr9:96927800-96931600	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr9:96927800-96931600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr9:96927800-96931600	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr9:96927800-96932200	Active TSS	HSMMtube	muscle
25	chr9:96927800-96932600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr9:96927800-96932600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:96927800-96932800	Active TSS	Aorta	Aorta
28	chr9:96927800-96933200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:96928000-96929600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:96928000-96929600	Active TSS	Gastric	stomach
31	chr9:96928000-96929800	Active TSS	Brain Hippocampus Middle	brain
32	chr9:96928000-96929800	Active TSS	Esophagus	oesophagus
33	chr9:96928000-96929800	Active TSS	Pancreas	Pancrea
34	chr9:96928000-96930200	Active TSS	Brain Cingulate Gyrus	brain
35	chr9:96928000-96930200	Active TSS	Placenta Amnion	Placenta Amnion
36	chr9:96928000-96930400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:96928000-96930400	Active TSS	Colon Smooth Muscle	Colon
38	chr9:96928000-96930400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr9:96928000-96930400	Active TSS	Small Intestine	intestine
40	chr9:96928000-96930600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr9:96928000-96930800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:96928000-96930800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:96928000-96930800	Active TSS	Duodenum Mucosa	Duodenum
44	chr9:96928000-96931000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr9:96928000-96931000	Active TSS	H9 Cell Line	embryonic stem cell
46	chr9:96928000-96931000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:96928000-96931000	Active TSS	HSMM	muscle
48	chr9:96928000-96931000	Active TSS	NHDF-Ad	bronchial
49	chr9:96928000-96931200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:96928000-96931200	Active TSS	Ovary	ovary

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