Variant report

Variant	rs511906
Chromosome Location	chr5:112136204-112136205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10051624	0.82[AMR][1000 genomes]
rs10071425	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11241183	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11241184	0.83[AMR][1000 genomes]
rs11241185	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11749701	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12518091	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12656359	0.85[EUR][1000 genomes]
rs12658609	0.82[AMR][1000 genomes]
rs13156251	0.88[AFR][1000 genomes]
rs1914	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1966476	0.81[ASN][1000 genomes]
rs1974786	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2019720	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2229992	0.83[ASN][1000 genomes]
rs2251913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253987	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2289484	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2431239	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2431241	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2431512	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431514	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439589	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2464803	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2545155	0.83[AMR][1000 genomes]
rs2545158	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2546106	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2546107	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2546108	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2546110	0.89[ASN][1000 genomes]
rs2546112	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2546117	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2707763	0.84[AMR][1000 genomes]
rs2707765	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28373740	0.84[AMR][1000 genomes]
rs28578275	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2901844	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351772	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35414976	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs382427	0.81[AMR][1000 genomes]
rs390092	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs395858	0.81[AMR][1000 genomes]
rs396321	0.81[AMR][1000 genomes]
rs41116	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs414098	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs448475	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs454886	0.80[ASN][1000 genomes]
rs458906	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs467033	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705486	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4705559	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4705573	0.82[AFR][1000 genomes]
rs4705608	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705610	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705624	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs518013	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548710	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs566419	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62364017	0.81[AMR][1000 genomes]
rs6594646	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6862050	0.81[AMR][1000 genomes]
rs6879057	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7704618	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9326863	0.82[AFR][1000 genomes]
rs9647582	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9647583	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][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	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs511906	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112100000-112152200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:112104600-112155400	Weak transcription	Psoas Muscle	Psoas
5	chr5:112115600-112140000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:112115800-112151200	Weak transcription	NHEK	skin
7	chr5:112118200-112136600	Weak transcription	Pancreas	Pancrea
8	chr5:112118200-112151200	Weak transcription	Gastric	stomach
9	chr5:112118200-112155600	Weak transcription	Right Ventricle	heart
10	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
11	chr5:112123600-112141800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:112124000-112144800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:112125000-112140000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:112126800-112142000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:112127800-112140000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:112129000-112144200	Weak transcription	Esophagus	oesophagus
17	chr5:112129000-112149800	Weak transcription	Left Ventricle	heart
18	chr5:112129000-112151600	Weak transcription	Hela-S3	cervix
19	chr5:112129000-112154600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:112129000-112157400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:112129400-112136600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:112129400-112163800	Weak transcription	Small Intestine	intestine
23	chr5:112129600-112163600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr5:112129800-112154800	Weak transcription	NH-A	brain
25	chr5:112130400-112145800	Weak transcription	Placenta	Placenta
26	chr5:112130600-112136600	Weak transcription	Brain Substantia Nigra	brain
27	chr5:112130600-112144000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:112130600-112150000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:112130600-112150200	Weak transcription	NHLF	lung
30	chr5:112130600-112154800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:112130600-112155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:112130600-112155600	Weak transcription	Fetal Heart	heart
33	chr5:112130800-112136600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:112130800-112138200	Weak transcription	HMEC	breast
35	chr5:112130800-112139800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:112130800-112143800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:112130800-112146600	Weak transcription	HSMMtube	muscle
38	chr5:112130800-112149800	Weak transcription	Lung	lung
39	chr5:112130800-112150000	Weak transcription	Spleen	Spleen
40	chr5:112130800-112150200	Weak transcription	Aorta	Aorta
41	chr5:112130800-112151200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:112130800-112151400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr5:112130800-112154800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:112130800-112155400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:112131000-112140800	Weak transcription	Osteobl	bone
46	chr5:112131000-112142400	Weak transcription	Fetal Intestine Small	intestine
47	chr5:112131000-112144200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:112131200-112138800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:112131200-112140000	Weak transcription	Fetal Stomach	stomach
50	chr5:112131200-112146400	Weak transcription	H9 Cell Line	embryonic stem cell

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