Variant report

Variant	rs2253987
Chromosome Location	chr5:112166862-112166863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10051624	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10071425	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10075281	0.81[AMR][1000 genomes]
rs10075323	0.81[AMR][1000 genomes]
rs10075377	0.81[AMR][1000 genomes]
rs10213844	0.82[AMR][1000 genomes]
rs11241183	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11241184	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11241185	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11749701	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12513787	0.82[AMR][1000 genomes]
rs12518091	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12656359	0.82[EUR][1000 genomes]
rs12658609	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13156251	0.83[AFR][1000 genomes]
rs1914	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1966476	0.93[ASN][1000 genomes]
rs1974786	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2019720	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2229992	0.94[ASN][1000 genomes]
rs2251913	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2289484	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2431239	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2431241	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2431512	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431514	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439589	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2464803	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2545155	0.85[AMR][1000 genomes]
rs2545158	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2546106	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2546107	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2546108	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2546110	0.91[ASN][1000 genomes]
rs2546112	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2546117	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2707763	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2707765	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28373740	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28578275	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2901844	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2909786	0.86[EUR][1000 genomes]
rs2909787	0.86[EUR][1000 genomes]
rs2909958	0.86[EUR][1000 genomes]
rs351772	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35414976	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs373059	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs382427	0.83[AMR][1000 genomes]
rs390092	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395858	0.83[AMR][1000 genomes]
rs396321	0.83[AMR][1000 genomes]
rs41116	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs414098	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs448475	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs458906	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs467033	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4705486	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4705559	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705573	0.82[AMR][1000 genomes]
rs4705608	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4705610	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4705624	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs511906	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs518013	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs548710	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs566419	0.85[AMR][1000 genomes]
rs569940	0.85[EUR][1000 genomes]
rs62364017	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6594646	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6862050	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6879057	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7704618	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9647582	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9647583	0.94[AMR][1000 genomes];0.88[EUR][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	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
5	nsv1034239	chr5:112161239-112194693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2253987	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
4	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:112151400-112176400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr5:112152000-112170400	Weak transcription	Brain Angular Gyrus	brain
12	chr5:112152000-112183800	Weak transcription	Gastric	stomach
13	chr5:112152200-112172000	Weak transcription	NHLF	lung
14	chr5:112153200-112169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:112154000-112175200	Weak transcription	Stomach Mucosa	stomach
18	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:112154600-112177800	Strong transcription	Primary T cells from cord blood	blood
20	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
21	chr5:112155200-112173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:112155800-112173400	Weak transcription	Pancreas	Pancrea
23	chr5:112155800-112173800	Weak transcription	Hela-S3	cervix
24	chr5:112156000-112173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:112156000-112173400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:112156000-112173400	Weak transcription	Fetal Heart	heart
27	chr5:112156200-112179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:112158600-112173200	Weak transcription	Fetal Kidney	kidney
29	chr5:112158800-112173400	Weak transcription	Fetal Brain Male	brain
30	chr5:112160600-112176200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:112160800-112168400	Strong transcription	Adipose Nuclei	Adipose
32	chr5:112160800-112168600	Strong transcription	Dnd41	blood
33	chr5:112160800-112168800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:112162000-112172800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:112162000-112175200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:112162400-112167800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:112162400-112168800	Strong transcription	Primary hematopoietic stem cells	blood
38	chr5:112162400-112171000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:112162600-112168000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:112162600-112174600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:112162800-112167600	Strong transcription	Primary B cells from cord blood	blood
42	chr5:112162800-112168400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:112162800-112168800	Strong transcription	Fetal Brain Female	brain
44	chr5:112162800-112169800	Strong transcription	Brain Hippocampus Middle	brain
45	chr5:112162800-112170000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:112162800-112170200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:112162800-112171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:112163000-112167400	Strong transcription	HSMM	muscle
49	chr5:112163000-112168400	Strong transcription	Brain Cingulate Gyrus	brain
50	chr5:112163400-112170200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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