Variant report

Variant	rs41116
Chromosome Location	chr5:112180921-112180922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112176263..112181367-chr5:112181688..112184725,5	K562	blood:
2	chr5:112089718..112092112-chr5:112180535..112183405,2	K562	blood:
3	chr5:112180772..112183270-chr5:112188278..112191041,2	K562	blood:
4	chr5:112180694..112183270-chr5:112188278..112192219,3	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10071425	0.83[EUR][1000 genomes]
rs1093611	0.83[ASN][1000 genomes]
rs11241183	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11241185	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12518091	0.84[EUR][1000 genomes]
rs153546	0.81[ASN][1000 genomes]
rs153548	0.81[ASN][1000 genomes]
rs153550	0.82[ASN][1000 genomes]
rs1914	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1966476	0.83[ASN][1000 genomes]
rs1974786	0.84[EUR][1000 genomes]
rs2019720	0.83[EUR][1000 genomes]
rs2229992	0.82[ASN][1000 genomes]
rs2251913	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2253987	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2431239	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2431241	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2431512	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2439589	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2464803	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2545155	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2545156	0.85[ASN][1000 genomes]
rs2545158	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2545170	0.82[ASN][1000 genomes]
rs2546106	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2546107	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2546108	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2546110	0.84[ASN][1000 genomes]
rs2546112	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2546117	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2707765	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28578275	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2901844	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2909786	0.81[EUR][1000 genomes]
rs2909787	0.81[EUR][1000 genomes]
rs2909958	0.81[EUR][1000 genomes]
rs3317	0.82[ASN][1000 genomes]
rs351767	0.85[ASN][1000 genomes]
rs351768	0.85[ASN][1000 genomes]
rs351770	0.87[ASN][1000 genomes]
rs351772	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35414976	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs368575	0.82[ASN][1000 genomes]
rs373059	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs374613	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs382427	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs390092	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs395858	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs410701	0.82[ASN][1000 genomes]
rs414098	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs419155	0.82[ASN][1000 genomes]
rs448162	0.98[ASN][1000 genomes]
rs448475	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448613	0.82[ASN][1000 genomes]
rs454968	0.93[ASN][1000 genomes]
rs458906	0.83[EUR][1000 genomes]
rs459102	0.83[ASN][1000 genomes]
rs460137	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs467033	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs469827	0.80[ASN][1000 genomes]
rs4705486	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4705608	0.84[EUR][1000 genomes]
rs4705610	0.84[EUR][1000 genomes]
rs4705624	0.85[EUR][1000 genomes]
rs495794	0.85[ASN][1000 genomes]
rs505382	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs511906	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs514763	0.84[ASN][1000 genomes]
rs518013	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs548710	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs566419	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6594646	0.84[EUR][1000 genomes]
rs6879057	0.83[EUR][1000 genomes]
rs712663	0.82[ASN][1000 genomes]
rs712670	0.82[ASN][1000 genomes]
rs7213	0.85[ASN][1000 genomes]
rs818429	0.83[ASN][1000 genomes]
rs9647582	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9647583	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41116	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:112152000-112183800	Weak transcription	Gastric	stomach
4	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
5	chr5:112163400-112183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:112165400-112182400	Weak transcription	Right Ventricle	heart
7	chr5:112174000-112182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:112174000-112182400	Weak transcription	Esophagus	oesophagus
9	chr5:112174000-112183800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:112174200-112181200	Weak transcription	Spleen	Spleen
11	chr5:112174200-112183800	Weak transcription	Hela-S3	cervix
12	chr5:112174400-112182400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:112174400-112183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:112174600-112183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:112174600-112184200	Weak transcription	Ovary	ovary
16	chr5:112174800-112183800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:112174800-112183800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:112174800-112183800	Weak transcription	NHEK	skin
19	chr5:112175200-112183800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:112175400-112183800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:112175400-112187600	Weak transcription	NHLF	lung
22	chr5:112175600-112182200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:112175600-112183800	Weak transcription	Psoas Muscle	Psoas
24	chr5:112175600-112183800	Weak transcription	GM12878-XiMat	blood
25	chr5:112175600-112184000	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:112175600-112184000	Weak transcription	Placenta	Placenta
27	chr5:112175800-112183600	Weak transcription	Liver	Liver
28	chr5:112175800-112183800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:112175800-112183800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:112175800-112183800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:112175800-112183800	Weak transcription	A549	lung
32	chr5:112175800-112183800	Weak transcription	Dnd41	blood
33	chr5:112176000-112181600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:112176000-112183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:112176000-112183800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:112176200-112181600	Weak transcription	Fetal Heart	heart
37	chr5:112176200-112182000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:112176200-112182200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:112176200-112182400	Weak transcription	Pancreas	Pancrea
40	chr5:112176200-112183800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:112176200-112183800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:112176200-112183800	Weak transcription	HUVEC	blood vessel
43	chr5:112176200-112183800	Weak transcription	NH-A	brain
44	chr5:112176200-112183800	Weak transcription	Osteobl	bone
45	chr5:112176200-112184000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:112176400-112182200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr5:112176400-112182200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:112176400-112182400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:112176400-112183600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr5:112176400-112183800	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links