Variant report

Variant	rs17116417
Chromosome Location	chr5:154145474-154145475
allele	A/G
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	chr5:154100501..154102218-chr5:154144697..154147317,2	K562	blood:
3	chr5:154132476..154143251-chr5:154145354..154162500,38	MCF-7	breast:
4	chr5:154144518..154146402-chr5:154237215..154238874,2	MCF-7	breast:

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

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1035368	1.00[TSI][hapmap]
rs10515727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12186480	0.86[ASN][1000 genomes]
rs12186610	0.88[EUR][1000 genomes]
rs12187572	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187890	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12187921	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12187934	0.82[ASN][1000 genomes]
rs12187974	0.86[ASN][1000 genomes]
rs12188149	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12188498	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189508	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12300	0.90[TSI][hapmap]
rs1421813	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17096232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116409	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17116421	1.00[TSI][hapmap]
rs17116433	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17116442	1.00[TSI][hapmap]
rs17116455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116534	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs17116638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17116669	0.82[ASN][1000 genomes]
rs1974776	1.00[TSI][hapmap]
rs1974777	1.00[TSI][hapmap]
rs2047305	1.00[JPT][hapmap]
rs2112223	1.00[CHB][hapmap]
rs2258437	1.00[TSI][hapmap]
rs2291780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2544880	1.00[TSI][hapmap]
rs2544884	1.00[TSI][hapmap]
rs2644743	1.00[TSI][hapmap]
rs2644744	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs2688198	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs2688201	1.00[TSI][hapmap]
rs2688208	1.00[CHB][hapmap]
rs28372688	0.86[ASN][1000 genomes]
rs348739	1.00[TSI][hapmap]
rs348750	1.00[TSI][hapmap]
rs348752	1.00[TSI][hapmap]
rs3776984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs39614	1.00[TSI][hapmap]
rs4452598	0.89[EUR][1000 genomes]
rs4626377	0.89[EUR][1000 genomes]
rs55692274	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56773390	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56895891	0.86[ASN][1000 genomes]
rs61145644	0.82[ASN][1000 genomes]
rs6580123	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6865950	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871813	0.82[ASN][1000 genomes]
rs6895588	0.82[ASN][1000 genomes]
rs6895702	0.82[ASN][1000 genomes]
rs6895741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs702742	1.00[TSI][hapmap]
rs73806917	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73807206	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807207	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807213	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807216	0.82[ASN][1000 genomes]
rs73809507	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7709899	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7716019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816717	1.00[TSI][hapmap]
rs816718	1.00[CHB][hapmap];0.94[TSI][hapmap]
rs816720	1.00[TSI][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17116417	CNOT8	cis	brain	seeQTL

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	chr5:154139600-154148600	Weak transcription	Fetal Intestine Large	intestine
10	chr5:154139800-154148800	Weak transcription	Fetal Brain Male	brain
11	chr5:154140000-154145800	Weak transcription	Fetal Stomach	stomach
12	chr5:154140200-154149200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:154140800-154146000	Weak transcription	NHDF-Ad	bronchial
14	chr5:154141000-154145600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:154141000-154145600	Weak transcription	Osteobl	bone
16	chr5:154141000-154145800	Weak transcription	Fetal Lung	lung
17	chr5:154141000-154148000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr5:154141000-154150000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr5:154141200-154145600	Weak transcription	NHEK	skin
20	chr5:154141200-154145800	Weak transcription	HMEC	breast
21	chr5:154141200-154146800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr5:154141200-154148800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:154141200-154150600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:154141200-154151000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:154141400-154145800	Weak transcription	Fetal Brain Female	brain
26	chr5:154141400-154146000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:154141400-154146400	Weak transcription	HUVEC	blood vessel
28	chr5:154141400-154146800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr5:154141400-154148800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:154141400-154148800	Weak transcription	Colonic Mucosa	Colon
31	chr5:154141400-154152200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:154141600-154146000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:154141600-154146000	Weak transcription	Esophagus	oesophagus
34	chr5:154141600-154146000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:154141600-154146800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:154142200-154145800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:154142200-154146000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr5:154142200-154146000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:154142200-154146600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:154142200-154148800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:154142200-154148800	Weak transcription	Aorta	Aorta
42	chr5:154142400-154145600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:154142400-154145600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:154142400-154145600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:154142400-154146200	Weak transcription	Brain Germinal Matrix	brain
46	chr5:154142400-154148800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr5:154142600-154145800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:154142600-154148800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:154142600-154149000	Weak transcription	Hela-S3	cervix
50	chr5:154142800-154148800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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