Variant report

Variant	rs27465
Chromosome Location	chr5:50086054-50086055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:50085830..50087662-chr5:50096625..50098199,2	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10035164	0.88[ASN][1000 genomes]
rs10036060	0.88[ASN][1000 genomes]
rs10038842	0.83[EUR][1000 genomes]
rs10039272	0.80[ASN][1000 genomes]
rs10039639	0.82[EUR][1000 genomes]
rs10043477	0.88[EUR][1000 genomes]
rs10044566	0.88[ASN][1000 genomes]
rs10051561	0.80[ASN][1000 genomes]
rs10054381	0.88[ASN][1000 genomes]
rs10056836	0.88[ASN][1000 genomes]
rs10059085	0.80[ASN][1000 genomes]
rs10060850	0.88[ASN][1000 genomes]
rs10065432	0.80[ASN][1000 genomes]
rs10070517	0.85[EUR][1000 genomes]
rs10072398	0.80[ASN][1000 genomes]
rs10075034	0.88[ASN][1000 genomes]
rs10085036	0.88[ASN][1000 genomes]
rs10471940	0.83[EUR][1000 genomes]
rs10471956	0.91[EUR][1000 genomes]
rs10755235	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10940472	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940497	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11739828	0.91[EUR][1000 genomes]
rs11750241	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11750771	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188262	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188654	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12519006	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521579	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654776	0.81[ASN][1000 genomes]
rs13153982	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13164951	0.86[EUR][1000 genomes]
rs13173734	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13359044	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361410	0.88[ASN][1000 genomes]
rs1375127	0.91[EUR][1000 genomes]
rs152102	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154133	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs154134	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs154135	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154137	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154138	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154140	1.00[ASN][1000 genomes]
rs154141	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157970	0.96[EUR][1000 genomes]
rs16884018	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs169497	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171555	0.99[EUR][1000 genomes]
rs17195388	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182230	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1988613	0.86[EUR][1000 genomes]
rs2354526	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548581	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548582	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548583	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256340	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256341	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2594706	0.92[ASN][1000 genomes]
rs26062	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26066	0.99[EUR][1000 genomes]
rs26068	0.99[EUR][1000 genomes]
rs26069	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697662	0.85[EUR][1000 genomes]
rs27156	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs27244	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs27245	0.96[EUR][1000 genomes]
rs27251	0.96[EUR][1000 genomes]
rs27254	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27264	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27357	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27468	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27469	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27574	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs27609	0.92[EUR][1000 genomes]
rs27627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27725	0.95[EUR][1000 genomes]
rs28085	0.95[EUR][1000 genomes]
rs282549	0.99[EUR][1000 genomes]
rs282550	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282551	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282552	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282553	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282557	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282559	0.93[EUR][1000 genomes]
rs282561	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28505342	0.80[ASN][1000 genomes]
rs28711235	0.80[ASN][1000 genomes]
rs32376	1.00[ASN][1000 genomes]
rs32377	0.99[EUR][1000 genomes]
rs32378	0.99[EUR][1000 genomes]
rs32404	0.88[ASN][1000 genomes]
rs32425	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763367	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs39613	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39949	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4029420	0.91[EUR][1000 genomes]
rs41502	0.92[EUR][1000 genomes]
rs42284	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865628	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57079776	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578198	0.88[EUR][1000 genomes]
rs59900589	0.83[EUR][1000 genomes]
rs62366937	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450301	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6450359	0.91[EUR][1000 genomes]
rs6869356	0.88[EUR][1000 genomes]
rs6872496	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6886872	0.91[EUR][1000 genomes]
rs6890519	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6890869	0.83[EUR][1000 genomes]
rs73101075	0.88[ASN][1000 genomes]
rs7449019	0.85[EUR][1000 genomes]
rs7711839	0.87[EUR][1000 genomes]
rs7728126	0.80[ASN][1000 genomes]
rs7734389	0.83[EUR][1000 genomes]
rs895801	0.91[EUR][1000 genomes]
rs921210	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598110	chr5:49988020-50089919	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv462163	chr5:49989701-50088317	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv598113	chr5:49989701-50088317	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv598114	chr5:49991561-50088317	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs27465	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs27465	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50041800-50090000	Weak transcription	Small Intestine	intestine
2	chr5:50052800-50098800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:50057800-50090600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:50058000-50090600	Weak transcription	Aorta	Aorta
6	chr5:50058200-50092400	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:50064000-50126800	Weak transcription	Osteobl	bone
8	chr5:50068800-50090600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:50069000-50086400	Weak transcription	Stomach Mucosa	stomach
10	chr5:50069600-50093400	Weak transcription	HMEC	breast
11	chr5:50069600-50095400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:50069600-50095400	Weak transcription	Fetal Lung	lung
13	chr5:50069600-50100000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:50070600-50098000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:50071400-50090600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:50071400-50093000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:50071400-50098200	Weak transcription	Fetal Intestine Small	intestine
18	chr5:50071400-50099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:50071400-50108000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr5:50071600-50086600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:50071600-50138200	Weak transcription	Placenta	Placenta
22	chr5:50072200-50093400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:50072400-50086400	Weak transcription	HSMMtube	muscle
24	chr5:50073400-50092400	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:50073600-50095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:50075200-50087000	Weak transcription	Fetal Kidney	kidney
27	chr5:50075200-50089200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:50075400-50092200	Weak transcription	Right Ventricle	heart
29	chr5:50076400-50090200	Weak transcription	Colonic Mucosa	Colon
30	chr5:50076600-50090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:50078000-50090600	Weak transcription	Esophagus	oesophagus
32	chr5:50078200-50140000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:50081000-50095000	Weak transcription	NHLF	lung
34	chr5:50081200-50092200	Strong transcription	Primary B cells from cord blood	blood
35	chr5:50081200-50098200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:50081400-50097400	Strong transcription	Primary T cells from cord blood	blood
37	chr5:50081400-50098200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:50081600-50086600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:50081600-50091200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:50081600-50098600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:50081600-50098800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:50081800-50095200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:50082200-50086400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:50082400-50095400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:50082800-50087200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr5:50083000-50090600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:50083000-50090600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:50083200-50090600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:50083200-50092200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr5:50083200-50092400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links