Variant report

Variant	rs465899
Chromosome Location	chr5:112177171-112177172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112176097..112178949-chr5:112179046..112180658,2	MCF-7	breast:
2	chr5:112070188..112073138-chr5:112174884..112177444,2	K562	blood:
3	chr5:112176263..112181367-chr5:112181688..112184725,5	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10463643	0.97[GIH][hapmap]
rs1069061	0.87[GIH][hapmap];0.80[MEX][hapmap]
rs1093611	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs1093677	0.94[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs12656359	0.90[ASN][1000 genomes]
rs12719151	0.82[MEX][hapmap]
rs1441375	0.84[CEU][hapmap]
rs1465910	0.85[CHB][hapmap]
rs149192	0.81[JPT][hapmap]
rs151976	0.86[ASN][1000 genomes]
rs151977	0.94[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs151978	0.86[ASN][1000 genomes]
rs153545	0.86[ASN][1000 genomes]
rs153548	0.84[CEU][hapmap]
rs1661035	0.88[CEU][hapmap];0.92[CHB][hapmap]
rs1734243	0.84[AMR][1000 genomes]
rs187075	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1966477	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2020383	0.93[CHB][hapmap]
rs2431238	0.97[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap]
rs2431240	0.86[ASN][1000 genomes]
rs2439591	0.85[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2464805	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs2545159	0.87[EUR][1000 genomes]
rs2545162	0.94[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2545163	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs2545164	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545165	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545166	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2545167	0.94[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2545169	0.88[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2546111	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2909786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2909787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2909904	0.89[ASN][1000 genomes]
rs2909958	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2952615	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351769	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs351770	0.84[CEU][hapmap]
rs351771	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35726351	0.87[ASN][1000 genomes]
rs372492	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs382260	0.94[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3846716	0.85[CHB][hapmap]
rs386830	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs392907	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs395266	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs397768	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs401908	0.83[EUR][1000 genomes]
rs4099181	0.93[CHB][hapmap]
rs41115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs411356	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs419632	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs42427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs429427	0.85[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs430665	0.84[CEU][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs431287	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs433429	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs434090	0.86[ASN][1000 genomes]
rs434157	0.87[GIH][hapmap];0.80[MEX][hapmap]
rs439456	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs446567	0.82[ASN][1000 genomes]
rs455412	0.91[CEU][hapmap];0.83[ASN][1000 genomes]
rs455469	0.86[ASN][1000 genomes]
rs456313	0.81[ASN][1000 genomes]
rs458451	0.84[CEU][hapmap];0.83[ASN][1000 genomes]
rs458967	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs460301	0.88[ASN][1000 genomes]
rs460832	0.87[CEU][hapmap];0.86[ASN][1000 genomes]
rs461424	0.82[ASN][1000 genomes]
rs461866	0.84[CEU][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs463229	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs464002	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs464708	0.88[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs465454	0.94[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs466443	0.85[CHB][hapmap]
rs468783	0.82[ASN][1000 genomes]
rs469663	0.86[ASN][1000 genomes]
rs469727	0.84[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs469760	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs469827	0.84[CEU][hapmap]
rs4705815	0.82[MEX][hapmap]
rs481789	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs497844	0.92[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501250	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs519397	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs529076	0.87[EUR][1000 genomes]
rs544243	0.81[MEX][hapmap]
rs563556	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs565453	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565603	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs569940	0.91[ASN][1000 genomes]
rs580237	0.89[ASN][1000 genomes]
rs6864688	0.93[CHB][hapmap]
rs6894351	0.85[CHB][hapmap]
rs6898133	0.92[CHB][hapmap]
rs698405	0.84[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs712662	0.84[CEU][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs712664	0.86[ASN][1000 genomes]
rs712665	0.84[CEU][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs712666	0.84[ASN][1000 genomes]
rs712668	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs712671	0.89[ASN][1000 genomes]
rs818423	0.87[ASN][1000 genomes]
rs818424	0.83[ASN][1000 genomes]
rs818425	0.83[ASN][1000 genomes]
rs861674	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs864682	0.87[ASN][1000 genomes]
rs866006	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9011	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs9326862	0.93[CHB][hapmap];0.88[CHD][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs465899	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs465899	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:112152000-112183800	Weak transcription	Gastric	stomach
6	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:112154600-112177800	Strong transcription	Primary T cells from cord blood	blood
10	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
11	chr5:112156200-112179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:112163400-112183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:112165400-112182400	Weak transcription	Right Ventricle	heart
14	chr5:112167800-112178000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:112168400-112178400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:112168400-112179000	Strong transcription	Fetal Muscle Leg	muscle
17	chr5:112170200-112177200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:112171400-112177400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:112171600-112179600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:112172200-112177400	Strong transcription	Fetal Thymus	thymus
21	chr5:112172400-112180000	Strong transcription	Fetal Brain Female	brain
22	chr5:112172600-112177800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:112172600-112179800	Strong transcription	HSMM	muscle
24	chr5:112172800-112178200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr5:112172800-112179000	Strong transcription	Brain Germinal Matrix	brain
26	chr5:112173200-112177200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:112173200-112177200	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr5:112173200-112177200	Strong transcription	Fetal Lung	lung
29	chr5:112173200-112177600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr5:112173200-112179200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:112173800-112177200	Strong transcription	HepG2	liver
32	chr5:112174000-112182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr5:112174000-112182400	Weak transcription	Esophagus	oesophagus
34	chr5:112174000-112183800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:112174200-112181200	Weak transcription	Spleen	Spleen
36	chr5:112174200-112183800	Weak transcription	Hela-S3	cervix
37	chr5:112174400-112182400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr5:112174400-112183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:112174600-112178600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:112174600-112183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:112174600-112184200	Weak transcription	Ovary	ovary
42	chr5:112174800-112179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:112174800-112183800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:112174800-112183800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:112174800-112183800	Weak transcription	NHEK	skin
46	chr5:112175000-112179000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr5:112175200-112178400	Weak transcription	HMEC	breast
48	chr5:112175200-112183800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr5:112175400-112178000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:112175400-112183800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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