Variant report

Variant	rs6882998
Chromosome Location	chr5:154144650-154144651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154133078..154137845-chr5:154142563..154149366,9	MCF-7	breast:
2	chr5:154026946..154029914-chr5:154142078..154144700,2	K562	blood:
3	chr5:154144518..154146402-chr5:154237215..154238874,2	MCF-7	breast:
4	chr5:154032703..154035820-chr5:154141862..154144774,3	K562	blood:

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13153640	0.84[TSI][hapmap]
rs13156669	1.00[AFR][1000 genomes]
rs13164115	0.90[CEU][hapmap]
rs13182236	0.85[TSI][hapmap]
rs1403559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2434217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2434218	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544869	0.83[MEX][hapmap]
rs2544891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs816723	0.83[MEX][hapmap]
rs816735	0.83[ASN][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	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6882998	CNOT8	cis	Thyroid	GTEx
rs6882998	CNOT8	cis	Artery Tibial	GTEx
rs6882998	CNOT8	cis	Adipose Subcutaneous	GTEx
rs6882998	CNOT8	cis	lung	GTEx
rs6882998	CNOT8	cis	Nerve Tibial	GTEx
rs6882998	CNOT8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154138200-154146000	Weak transcription	Placenta	Placenta
2	chr5:154138200-154151400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr5:154138200-154156000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr5:154138400-154147800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:154138800-154150000	Weak transcription	HSMM	muscle
6	chr5:154139000-154147200	Weak transcription	NH-A	brain
7	chr5:154139000-154149800	Weak transcription	NHLF	lung
8	chr5:154139200-154145600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:154139400-154145400	Weak transcription	Fetal Kidney	kidney
10	chr5:154139600-154148600	Weak transcription	Fetal Intestine Large	intestine
11	chr5:154139800-154148800	Weak transcription	Fetal Brain Male	brain
12	chr5:154140000-154145800	Weak transcription	Fetal Stomach	stomach
13	chr5:154140200-154149200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:154140800-154146000	Weak transcription	NHDF-Ad	bronchial
15	chr5:154141000-154144800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr5:154141000-154145600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:154141000-154145600	Weak transcription	Osteobl	bone
18	chr5:154141000-154145800	Weak transcription	Fetal Lung	lung
19	chr5:154141000-154148000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:154141000-154150000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr5:154141200-154144800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr5:154141200-154145400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:154141200-154145600	Weak transcription	NHEK	skin
24	chr5:154141200-154145800	Weak transcription	HMEC	breast
25	chr5:154141200-154146800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr5:154141200-154148800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:154141200-154150600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:154141200-154151000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:154141400-154145000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:154141400-154145800	Weak transcription	Fetal Brain Female	brain
31	chr5:154141400-154146000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:154141400-154146400	Weak transcription	HUVEC	blood vessel
33	chr5:154141400-154146800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr5:154141400-154148800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:154141400-154148800	Weak transcription	Colonic Mucosa	Colon
36	chr5:154141400-154152200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:154141600-154146000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:154141600-154146000	Weak transcription	Esophagus	oesophagus
39	chr5:154141600-154146000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:154141600-154146800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:154142000-154144800	Weak transcription	Primary B cells from cord blood	blood
42	chr5:154142000-154144800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:154142200-154144800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:154142200-154144800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:154142200-154144800	Weak transcription	Right Ventricle	heart
46	chr5:154142200-154145800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr5:154142200-154146000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr5:154142200-154146000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:154142200-154146600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:154142200-154148800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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