Variant report

Variant	rs12656359
Chromosome Location	chr5:112151551-112151552
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr5:112151547-112151836	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111908035..111909669-chr5:112150477..112152951,2	K562	blood:

Variant related genes	Relation type
APC	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10073398	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10076641	0.80[EUR][1000 genomes]
rs11241184	0.80[EUR][1000 genomes]
rs11954856	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12659119	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1465910	0.81[EUR][1000 genomes]
rs1816769	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs187075	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1914	0.85[EUR][1000 genomes]
rs1966477	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2020383	0.85[EUR][1000 genomes]
rs2251913	0.85[EUR][1000 genomes]
rs2253987	0.82[EUR][1000 genomes]
rs2289484	0.82[EUR][1000 genomes]
rs2431240	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2431241	0.84[EUR][1000 genomes]
rs2431242	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2545158	0.84[EUR][1000 genomes]
rs2545162	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2545164	0.99[ASN][1000 genomes]
rs2545165	0.99[ASN][1000 genomes]
rs2545166	0.81[ASN][1000 genomes]
rs2545167	0.81[ASN][1000 genomes]
rs2546106	0.85[EUR][1000 genomes]
rs2546107	0.83[EUR][1000 genomes]
rs2546108	0.81[EUR][1000 genomes]
rs2707763	0.82[EUR][1000 genomes]
rs2909786	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2909787	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2909904	0.81[ASN][1000 genomes]
rs2909958	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952615	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35130225	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs351769	0.80[ASN][1000 genomes]
rs351771	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs351772	0.81[EUR][1000 genomes]
rs382260	0.81[ASN][1000 genomes]
rs386830	0.88[ASN][1000 genomes]
rs390092	0.85[EUR][1000 genomes]
rs397768	0.91[ASN][1000 genomes]
rs4099181	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41115	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs411356	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs42427	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs429427	0.82[ASN][1000 genomes]
rs433429	0.88[ASN][1000 genomes]
rs439456	0.81[ASN][1000 genomes]
rs460301	0.80[ASN][1000 genomes]
rs463229	0.80[ASN][1000 genomes]
rs464708	0.99[ASN][1000 genomes]
rs465899	0.90[ASN][1000 genomes]
rs4705609	0.82[EUR][1000 genomes]
rs481789	0.86[ASN][1000 genomes]
rs497844	0.83[ASN][1000 genomes]
rs501250	0.81[AFR][1000 genomes]
rs511906	0.85[EUR][1000 genomes]
rs518013	0.85[EUR][1000 genomes]
rs544243	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs565453	0.86[ASN][1000 genomes]
rs565603	0.83[ASN][1000 genomes]
rs569940	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs580237	0.83[ASN][1000 genomes]
rs62364017	0.83[EUR][1000 genomes]
rs6867243	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6894351	0.81[EUR][1000 genomes]
rs712671	0.81[ASN][1000 genomes]
rs861674	0.81[EUR][1000 genomes]
rs866006	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9011	0.81[ASN][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
rs12656359	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr5:112118200-112155600	Weak transcription	Right Ventricle	heart
6	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
7	chr5:112129000-112151600	Weak transcription	Hela-S3	cervix
8	chr5:112129000-112154600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:112129000-112157400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:112129400-112163800	Weak transcription	Small Intestine	intestine
11	chr5:112129600-112163600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:112129800-112154800	Weak transcription	NH-A	brain
13	chr5:112130600-112154800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:112130600-112155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:112130600-112155600	Weak transcription	Fetal Heart	heart
16	chr5:112130800-112154800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:112130800-112155400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:112131800-112157800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:112131800-112164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:112132000-112154800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:112132200-112155200	Weak transcription	Fetal Brain Male	brain
23	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:112133400-112154800	Weak transcription	HepG2	liver
25	chr5:112133600-112160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:112133600-112161400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:112134000-112153600	Weak transcription	NHDF-Ad	bronchial
28	chr5:112134000-112162800	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr5:112137000-112154800	Weak transcription	HUVEC	blood vessel
31	chr5:112139000-112151600	Weak transcription	HMEC	breast
32	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:112141400-112162400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:112142000-112151600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:112143600-112159800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:112144200-112152200	Strong transcription	Fetal Brain Female	brain
37	chr5:112144200-112159800	Strong transcription	HSMM	muscle
38	chr5:112144800-112152000	Strong transcription	Primary T cells from cord blood	blood
39	chr5:112145400-112152000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr5:112145400-112165600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:112145600-112156600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:112146200-112152400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:112146200-112165800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr5:112147400-112153400	Weak transcription	Fetal Lung	lung
45	chr5:112147600-112151600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:112147800-112154600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:112147800-112154600	Weak transcription	Esophagus	oesophagus
48	chr5:112147800-112154800	Weak transcription	Brain Germinal Matrix	brain
49	chr5:112147800-112154800	Weak transcription	Fetal Kidney	kidney
50	chr5:112147800-112154800	Weak transcription	HSMMtube	muscle

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