Variant report

Variant	rs12659119
Chromosome Location	chr5:112101457-112101458
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10071425	0.85[EUR][1000 genomes]
rs10073398	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10076641	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11241182	0.83[EUR][1000 genomes]
rs11241183	0.86[EUR][1000 genomes]
rs11241184	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11241185	0.87[EUR][1000 genomes]
rs11749632	0.81[EUR][1000 genomes]
rs11749701	0.82[EUR][1000 genomes]
rs11954856	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12513804	0.90[EUR][1000 genomes]
rs12518091	0.85[EUR][1000 genomes]
rs12656359	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12658609	0.80[EUR][1000 genomes]
rs12719151	0.85[EUR][1000 genomes]
rs1465910	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1816769	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1974786	0.86[EUR][1000 genomes]
rs2019720	0.85[EUR][1000 genomes]
rs2020383	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289484	0.94[EUR][1000 genomes]
rs2431239	0.87[EUR][1000 genomes]
rs2431240	0.83[AMR][1000 genomes]
rs2431242	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2431512	0.87[EUR][1000 genomes]
rs2431514	0.82[EUR][1000 genomes]
rs2439589	0.87[EUR][1000 genomes]
rs2439591	0.96[ASN][1000 genomes]
rs2546108	0.80[EUR][1000 genomes]
rs2546117	0.87[EUR][1000 genomes]
rs2707763	0.94[EUR][1000 genomes]
rs2707765	0.85[EUR][1000 genomes]
rs28373740	0.80[EUR][1000 genomes]
rs28578275	0.86[EUR][1000 genomes]
rs2900066	0.86[EUR][1000 genomes]
rs2901844	0.85[EUR][1000 genomes]
rs2909786	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2909787	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2909958	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35130225	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs351772	0.81[EUR][1000 genomes]
rs35414976	0.87[EUR][1000 genomes]
rs3846716	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs396321	0.88[EUR][1000 genomes]
rs4099181	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs414098	0.84[EUR][1000 genomes]
rs458906	0.85[EUR][1000 genomes]
rs464002	0.82[ASN][1000 genomes]
rs467033	0.86[EUR][1000 genomes]
rs4705486	0.86[EUR][1000 genomes]
rs4705559	0.81[EUR][1000 genomes]
rs4705608	0.86[EUR][1000 genomes]
rs4705609	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705610	0.86[EUR][1000 genomes]
rs4705624	0.86[EUR][1000 genomes]
rs4705815	0.85[EUR][1000 genomes]
rs4705816	0.85[EUR][1000 genomes]
rs544243	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs548710	0.81[EUR][1000 genomes]
rs569940	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62364017	0.94[EUR][1000 genomes]
rs6594643	0.86[EUR][1000 genomes]
rs6594644	0.85[EUR][1000 genomes]
rs6594646	0.86[EUR][1000 genomes]
rs6864688	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6867243	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879057	0.86[EUR][1000 genomes]
rs6894351	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6898133	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7704618	0.81[EUR][1000 genomes]
rs861674	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9326862	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326863	0.88[EUR][1000 genomes]
rs953916	0.83[EUR][1000 genomes]
rs9647582	0.86[EUR][1000 genomes]
rs9647583	0.86[EUR][1000 genomes]
rs971517	0.86[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	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
rs12659119	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112074400-112102800	Weak transcription	Fetal Stomach	stomach
2	chr5:112074400-112103400	Weak transcription	Left Ventricle	heart
3	chr5:112074400-112119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:112074600-112103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:112075200-112103000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:112075400-112101600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:112079600-112128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:112079800-112128600	Weak transcription	Small Intestine	intestine
11	chr5:112081200-112128600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:112084400-112103000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:112084600-112103200	Weak transcription	Psoas Muscle	Psoas
14	chr5:112087600-112117600	Weak transcription	Gastric	stomach
15	chr5:112089800-112116600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:112093400-112102800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:112093400-112103200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:112093400-112103200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:112093400-112103200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:112093400-112103400	Weak transcription	Thymus	Thymus
21	chr5:112093400-112103600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr5:112093400-112103800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:112093400-112103800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:112093400-112108600	Weak transcription	Brain Angular Gyrus	brain
25	chr5:112093400-112114800	Weak transcription	Brain Substantia Nigra	brain
26	chr5:112093400-112114800	Weak transcription	NHEK	skin
27	chr5:112093400-112116000	Weak transcription	HUVEC	blood vessel
28	chr5:112093400-112117400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:112093400-112128600	Weak transcription	Ovary	ovary
30	chr5:112093400-112128600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:112093600-112103400	Weak transcription	Fetal Kidney	kidney
33	chr5:112093800-112102200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:112094200-112102800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:112094200-112128600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:112094200-112128800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:112095200-112122400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:112095400-112102800	Weak transcription	Fetal Intestine Small	intestine
39	chr5:112095600-112104600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:112095600-112116800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:112096200-112102000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:112096200-112102600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:112096200-112102600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr5:112096200-112102800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:112096200-112102800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:112096200-112103400	Weak transcription	Fetal Muscle Leg	muscle
47	chr5:112096200-112105000	Weak transcription	Fetal Lung	lung
48	chr5:112096200-112116000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:112096200-112117600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:112096400-112102000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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