Variant report

Variant	rs851180
Chromosome Location	chr1:223306354-223306355
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223301112..223303740-chr1:223305337..223308068,3	MCF-7	breast:
2	chr1:223305860..223308306-chr1:223535536..223539484,5	MCF-7	breast:
3	chr1:223306168..223308719-chr1:223316086..223318176,3	MCF-7	breast:
4	chr1:223306279..223308015-chr1:223870177..223873121,2	MCF-7	breast:
5	chr1:223297874..223300062-chr1:223305368..223307406,3	MCF-7	breast:
6	chr1:223305699..223307476-chr1:223314416..223316383,2	K562	blood:
7	chr1:223301561..223303590-chr1:223305260..223306850,2	K562	blood:
8	chr1:223304714..223306569-chr1:223385509..223387660,2	MCF-7	breast:
9	chr1:223305679..223307985-chr1:223321092..223323680,2	K562	blood:
10	chr1:223305268..223307186-chr1:223856777..223859694,2	K562	blood:
11	chr1:223305214..223307965-chr1:223314380..223316751,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236846	Chromatin interaction
ENSG00000187554	Chromatin interaction
ENSG00000143502	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10443637	0.91[EUR][1000 genomes]
rs10443638	0.91[EUR][1000 genomes]
rs10443639	0.91[EUR][1000 genomes]
rs10443640	0.91[EUR][1000 genomes]
rs1100886	0.80[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1100887	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12729658	0.91[EUR][1000 genomes]
rs12748315	0.91[EUR][1000 genomes]
rs1341987	0.89[JPT][hapmap];0.83[MEX][hapmap]
rs1640840	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1773714	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1773718	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1773726	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1773727	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1773729	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1861172	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2096141	0.89[JPT][hapmap]
rs2096142	0.89[JPT][hapmap]
rs2353476	0.89[JPT][hapmap]
rs2430402	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2430403	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2487831	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2487833	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28460738	0.81[EUR][1000 genomes]
rs28499047	0.81[EUR][1000 genomes]
rs28522106	0.91[EUR][1000 genomes]
rs28594689	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28691199	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28880136	0.91[EUR][1000 genomes]
rs34253986	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35251562	0.95[EUR][1000 genomes]
rs3795742	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3795743	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4661281	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4661282	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744113	0.83[MEX][hapmap]
rs5744174	0.90[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61840078	0.82[EUR][1000 genomes]
rs61840137	0.91[EUR][1000 genomes]
rs61840138	0.95[EUR][1000 genomes]
rs61840140	0.91[EUR][1000 genomes]
rs61840141	0.91[EUR][1000 genomes]
rs61840142	0.91[EUR][1000 genomes]
rs712866	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7547359	0.90[EUR][1000 genomes]
rs851134	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs851135	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851136	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs851137	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851138	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851139	0.93[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs851178	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851179	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851181	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851183	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851184	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851185	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851186	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs851187	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851188	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs851189	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851190	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs851192	0.90[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851193	0.90[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs864834	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs877327	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs887947	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs851180	TLR5	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223277000-223306800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223297200-223307000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:223297200-223307000	Weak transcription	Aorta	Aorta
4	chr1:223297600-223306800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:223302600-223306400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:223302800-223306800	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:223303000-223306600	Weak transcription	Lung	lung
8	chr1:223303000-223306800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:223303000-223306800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:223303000-223306800	Weak transcription	Esophagus	oesophagus
11	chr1:223303000-223306800	Weak transcription	Psoas Muscle	Psoas
12	chr1:223303000-223306800	Weak transcription	Right Atrium	heart
13	chr1:223303000-223306800	Weak transcription	Stomach Mucosa	stomach
14	chr1:223303000-223307400	Weak transcription	Left Ventricle	heart
15	chr1:223303200-223306600	Weak transcription	Liver	Liver
16	chr1:223303200-223306600	Weak transcription	Brain Angular Gyrus	brain
17	chr1:223303200-223306600	Weak transcription	Pancreas	Pancrea
18	chr1:223303200-223306600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:223303200-223306600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:223303200-223306800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:223303200-223306800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:223303200-223306800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:223303200-223306800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:223303200-223306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:223303200-223306800	Weak transcription	Adipose Nuclei	Adipose
26	chr1:223303200-223306800	Weak transcription	Colonic Mucosa	Colon
27	chr1:223303200-223306800	Weak transcription	Gastric	stomach
28	chr1:223303200-223306800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:223303200-223306800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:223303200-223306800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:223303200-223307000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:223303200-223307000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
34	chr1:223303400-223306400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:223303400-223306600	Weak transcription	Brain Anterior Caudate	brain
36	chr1:223303600-223306600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:223303800-223307000	Weak transcription	NHEK	skin
38	chr1:223304000-223306800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:223304800-223306600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:223305200-223306800	Weak transcription	Ovary	ovary
41	chr1:223306000-223306800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:223306200-223306600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
43	chr1:223306200-223306600	Enhancers	Duodenum Mucosa	Duodenum

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