Variant report

Variant	rs2431239
Chromosome Location	chr5:112103680-112103681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10051624	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10071425	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10072068	0.83[EUR][1000 genomes]
rs10073398	0.84[EUR][1000 genomes]
rs10075281	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10075323	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10075377	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10213844	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10477483	0.84[EUR][1000 genomes]
rs11241183	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241184	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11241185	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11749701	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11954856	0.85[EUR][1000 genomes]
rs12332692	0.83[EUR][1000 genomes]
rs12513787	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12518091	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12658609	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12659119	0.87[EUR][1000 genomes]
rs13156251	0.84[EUR][1000 genomes]
rs1441367	0.82[EUR][1000 genomes]
rs1465910	0.80[EUR][1000 genomes]
rs1530256	0.83[EUR][1000 genomes]
rs17285505	0.81[EUR][1000 genomes]
rs1816769	0.86[EUR][1000 genomes]
rs1866924	0.83[EUR][1000 genomes]
rs1914	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1968557	0.83[EUR][1000 genomes]
rs1974786	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2019720	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2020383	0.84[EUR][1000 genomes]
rs2099810	0.84[EUR][1000 genomes]
rs2229992	0.80[ASN][1000 genomes]
rs2251913	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2253987	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2289484	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2431241	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2431242	0.86[EUR][1000 genomes]
rs2431512	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431514	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2439589	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464803	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2545158	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2546106	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2546107	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2546108	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2546117	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707763	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2707765	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28373740	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28578275	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901844	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909786	0.81[EUR][1000 genomes]
rs2909787	0.81[EUR][1000 genomes]
rs2909958	0.81[EUR][1000 genomes]
rs35130225	0.86[EUR][1000 genomes]
rs351772	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35414976	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390092	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs396321	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4099181	0.85[EUR][1000 genomes]
rs41116	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs414098	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs448475	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs458906	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467033	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705486	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4705559	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4705573	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4705608	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4705609	0.81[EUR][1000 genomes]
rs4705610	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4705624	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511906	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs518013	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs548710	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs569940	0.80[EUR][1000 genomes]
rs62364017	0.90[EUR][1000 genomes]
rs6594646	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6862050	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6864688	0.86[EUR][1000 genomes]
rs6867243	0.85[EUR][1000 genomes]
rs6879057	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6894351	0.80[EUR][1000 genomes]
rs7704618	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7727738	0.81[EUR][1000 genomes]
rs861674	0.81[EUR][1000 genomes]
rs9326862	0.83[EUR][1000 genomes]
rs9326863	0.85[EUR][1000 genomes]
rs9647582	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9647583	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2431239	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112074400-112119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:112079600-112128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:112079800-112128600	Weak transcription	Small Intestine	intestine
6	chr5:112081200-112128600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:112087600-112117600	Weak transcription	Gastric	stomach
8	chr5:112089800-112116600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:112093400-112103800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:112093400-112103800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:112093400-112108600	Weak transcription	Brain Angular Gyrus	brain
12	chr5:112093400-112114800	Weak transcription	Brain Substantia Nigra	brain
13	chr5:112093400-112114800	Weak transcription	NHEK	skin
14	chr5:112093400-112116000	Weak transcription	HUVEC	blood vessel
15	chr5:112093400-112117400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:112093400-112128600	Weak transcription	Ovary	ovary
17	chr5:112093400-112128600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:112094200-112128600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:112094200-112128800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:112095200-112122400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:112095600-112104600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:112095600-112116800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:112096200-112105000	Weak transcription	Fetal Lung	lung
25	chr5:112096200-112116000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr5:112096200-112117600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:112096400-112103800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr5:112096400-112106200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:112096400-112106600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:112096400-112109200	Weak transcription	GM12878-XiMat	blood
31	chr5:112096400-112115400	Weak transcription	K562	blood
32	chr5:112097000-112116600	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:112097800-112127000	Weak transcription	Esophagus	oesophagus
34	chr5:112098000-112128600	Weak transcription	HepG2	liver
35	chr5:112098200-112106800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:112098200-112107600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:112098200-112114600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:112098200-112114600	Weak transcription	HMEC	breast
39	chr5:112098200-112128600	Weak transcription	Aorta	Aorta
40	chr5:112098200-112129800	Weak transcription	Spleen	Spleen
41	chr5:112098400-112106800	Weak transcription	NHLF	lung
42	chr5:112098400-112130000	Weak transcription	Fetal Heart	heart
43	chr5:112098600-112106400	Weak transcription	NHDF-Ad	bronchial
44	chr5:112098600-112106800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr5:112098600-112113600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:112098600-112116400	Weak transcription	Placenta	Placenta
47	chr5:112098600-112131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr5:112098800-112113600	Weak transcription	HSMMtube	muscle
49	chr5:112098800-112122400	Weak transcription	A549	lung
50	chr5:112099200-112107200	Weak transcription	Fetal Brain Male	brain

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