Variant report

Variant	rs2431242
Chromosome Location	chr5:112118195-112118196
allele	A/G
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	POLR2A	chr5:112117810-112118278	K562	blood:	n/a	n/a

Variant related genes	Relation type
CBX3P3	TF binding region

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

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10071425	0.83[EUR][1000 genomes]
rs10073398	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10076641	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11241182	0.80[EUR][1000 genomes]
rs11241183	0.84[EUR][1000 genomes]
rs11241184	0.90[EUR][1000 genomes]
rs11241185	0.86[EUR][1000 genomes]
rs11749632	0.82[EUR][1000 genomes]
rs11749701	0.80[EUR][1000 genomes]
rs11954856	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12513804	0.89[EUR][1000 genomes]
rs12518091	0.83[EUR][1000 genomes]
rs12656359	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12659119	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12719151	0.85[EUR][1000 genomes]
rs1465910	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1734243	0.83[ASN][1000 genomes]
rs1816769	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1974786	0.84[EUR][1000 genomes]
rs2019720	0.84[EUR][1000 genomes]
rs2020383	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2289484	0.92[EUR][1000 genomes]
rs2431239	0.86[EUR][1000 genomes]
rs2431240	0.84[AMR][1000 genomes]
rs2431512	0.86[EUR][1000 genomes]
rs2431514	0.83[EUR][1000 genomes]
rs2439589	0.86[EUR][1000 genomes]
rs2545163	0.82[ASN][1000 genomes]
rs2546108	0.80[EUR][1000 genomes]
rs2546117	0.86[EUR][1000 genomes]
rs2707763	0.92[EUR][1000 genomes]
rs2707765	0.85[EUR][1000 genomes]
rs28578275	0.84[EUR][1000 genomes]
rs2900066	0.85[EUR][1000 genomes]
rs2901844	0.83[EUR][1000 genomes]
rs2909786	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2909787	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2909958	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35130225	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35414976	0.86[EUR][1000 genomes]
rs3846716	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs395266	0.83[ASN][1000 genomes]
rs396321	0.87[EUR][1000 genomes]
rs401908	0.83[ASN][1000 genomes]
rs4099181	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs414098	0.83[EUR][1000 genomes]
rs458906	0.85[EUR][1000 genomes]
rs467033	0.85[EUR][1000 genomes]
rs4705486	0.84[EUR][1000 genomes]
rs4705608	0.84[EUR][1000 genomes]
rs4705609	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4705610	0.84[EUR][1000 genomes]
rs4705624	0.84[EUR][1000 genomes]
rs4705815	0.85[EUR][1000 genomes]
rs4705816	0.85[EUR][1000 genomes]
rs501250	0.83[ASN][1000 genomes]
rs529076	0.83[ASN][1000 genomes]
rs544243	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs569940	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62364017	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6594643	0.85[EUR][1000 genomes]
rs6594644	0.83[EUR][1000 genomes]
rs6594646	0.83[EUR][1000 genomes]
rs6864688	0.84[EUR][1000 genomes]
rs6867243	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6879057	0.83[EUR][1000 genomes]
rs6894351	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6898133	0.86[EUR][1000 genomes]
rs861674	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9326862	0.89[EUR][1000 genomes]
rs9326863	0.85[EUR][1000 genomes]
rs953916	0.81[EUR][1000 genomes]
rs9647582	0.84[EUR][1000 genomes]
rs9647583	0.83[EUR][1000 genomes]
rs971517	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	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
7	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
rs2431242	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	chr5:112074400-112119800	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	chr5:112093400-112128600	Weak transcription	Ovary	ovary
8	chr5:112093400-112128600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:112094200-112128600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:112094200-112128800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:112095200-112122400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:112097800-112127000	Weak transcription	Esophagus	oesophagus
14	chr5:112098000-112128600	Weak transcription	HepG2	liver
15	chr5:112098200-112128600	Weak transcription	Aorta	Aorta
16	chr5:112098200-112129800	Weak transcription	Spleen	Spleen
17	chr5:112098400-112130000	Weak transcription	Fetal Heart	heart
18	chr5:112098600-112131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:112098800-112122400	Weak transcription	A549	lung
20	chr5:112099600-112122200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:112100000-112152200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:112102200-112120400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:112102400-112118400	Strong transcription	Dnd41	blood
24	chr5:112102400-112121000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:112102600-112118400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr5:112102800-112119000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:112104400-112125600	Weak transcription	Fetal Intestine Small	intestine
29	chr5:112104600-112128600	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:112104600-112155400	Weak transcription	Psoas Muscle	Psoas
31	chr5:112104800-112128000	Weak transcription	Hela-S3	cervix
32	chr5:112104800-112130800	Weak transcription	Stomach Mucosa	stomach
33	chr5:112105000-112128600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr5:112105000-112128600	Weak transcription	Thymus	Thymus
35	chr5:112105200-112125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:112108200-112129200	Weak transcription	NH-A	brain
37	chr5:112108400-112130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:112109200-112120800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:112110200-112118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:112110400-112128800	Weak transcription	Brain Angular Gyrus	brain
41	chr5:112111000-112128600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:112111200-112118200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:112111200-112118200	Strong transcription	Fetal Thymus	thymus
44	chr5:112111400-112118400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:112111800-112118400	Strong transcription	Brain Anterior Caudate	brain
46	chr5:112112200-112118400	Strong transcription	Fetal Muscle Leg	muscle
47	chr5:112112200-112128400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:112112200-112128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:112113400-112122200	Strong transcription	Primary B cells from cord blood	blood
50	chr5:112113600-112118200	Strong transcription	Fetal Intestine Large	intestine

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