Variant report

Variant	rs154141
Chromosome Location	chr5:50069767-50069768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	0.84[EUR][1000 genomes]
rs10039272	0.80[ASN][1000 genomes]
rs10039639	0.83[EUR][1000 genomes]
rs10043477	0.89[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	0.86[EUR][1000 genomes]
rs10072398	0.80[ASN][1000 genomes]
rs10075034	0.88[ASN][1000 genomes]
rs10085036	0.88[ASN][1000 genomes]
rs10471940	0.84[EUR][1000 genomes]
rs10471956	0.92[EUR][1000 genomes]
rs10755235	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10940472	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940497	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11739828	0.92[EUR][1000 genomes]
rs11750241	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11750771	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188262	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188654	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12519006	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521579	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654776	0.81[ASN][1000 genomes]
rs13153982	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13164951	0.87[EUR][1000 genomes]
rs13173734	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13359044	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361410	0.88[ASN][1000 genomes]
rs1375127	0.92[EUR][1000 genomes]
rs152102	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154133	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs154134	1.00[ASN][1000 genomes]
rs154135	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154137	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154138	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154140	1.00[ASN][1000 genomes]
rs157970	0.97[EUR][1000 genomes]
rs16884018	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs169497	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171555	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17195388	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182230	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1988613	0.87[EUR][1000 genomes]
rs2354526	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548581	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548582	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548583	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256340	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256341	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2594706	0.92[ASN][1000 genomes]
rs26062	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26065	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26066	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26068	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26069	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26071	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697662	0.86[EUR][1000 genomes]
rs27156	0.95[EUR][1000 genomes]
rs27244	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27245	0.97[EUR][1000 genomes]
rs27251	0.97[EUR][1000 genomes]
rs27254	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27264	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27357	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27465	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27468	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27469	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27574	0.95[EUR][1000 genomes]
rs27609	0.91[EUR][1000 genomes]
rs27627	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27725	0.96[EUR][1000 genomes]
rs28085	0.96[EUR][1000 genomes]
rs282549	1.00[EUR][1000 genomes]
rs282550	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282551	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282552	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282553	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282557	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282559	0.95[EUR][1000 genomes]
rs282561	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[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	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32378	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32404	0.88[ASN][1000 genomes]
rs32425	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763367	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs39613	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39949	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4029420	0.92[EUR][1000 genomes]
rs41502	0.91[EUR][1000 genomes]
rs42284	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865628	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57079776	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578198	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59900589	0.84[EUR][1000 genomes]
rs62366937	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450301	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6450359	0.92[EUR][1000 genomes]
rs6869356	0.90[EUR][1000 genomes]
rs6872496	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6886872	0.92[EUR][1000 genomes]
rs6890519	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6890869	0.82[EUR][1000 genomes]
rs73101075	0.88[ASN][1000 genomes]
rs7449019	0.86[EUR][1000 genomes]
rs7711839	0.88[EUR][1000 genomes]
rs7728126	0.80[ASN][1000 genomes]
rs7734389	0.84[EUR][1000 genomes]
rs895801	0.92[EUR][1000 genomes]
rs921210	0.90[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
rs154141	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs154141	PARP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50041800-50070200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:50041800-50090000	Weak transcription	Small Intestine	intestine
3	chr5:50051200-50084600	Weak transcription	NHEK	skin
4	chr5:50052000-50078000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:50052800-50098800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:50056600-50070000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:50057800-50084600	Weak transcription	Ovary	ovary
9	chr5:50057800-50090600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:50058000-50070000	Weak transcription	Lung	lung
11	chr5:50058000-50090600	Weak transcription	Aorta	Aorta
12	chr5:50058200-50070800	Weak transcription	Spleen	Spleen
13	chr5:50058200-50075200	Weak transcription	Gastric	stomach
14	chr5:50058200-50084600	Weak transcription	Fetal Thymus	thymus
15	chr5:50058200-50092400	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:50060200-50084600	Weak transcription	Thymus	Thymus
17	chr5:50060400-50073400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:50060400-50081800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:50062200-50070000	Weak transcription	Pancreas	Pancrea
20	chr5:50063200-50082800	Weak transcription	Fetal Heart	heart
21	chr5:50063800-50070400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr5:50064000-50084400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:50064000-50126800	Weak transcription	Osteobl	bone
24	chr5:50066800-50084200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:50067200-50070200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:50067200-50071400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:50067600-50070200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr5:50067800-50069800	ZNF genes & repeats	Dnd41	blood
29	chr5:50067800-50070200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
30	chr5:50067800-50075400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:50068000-50072800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:50068000-50084600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:50068200-50077800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:50068800-50070200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:50068800-50090600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:50069000-50086400	Weak transcription	Stomach Mucosa	stomach
37	chr5:50069200-50071400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr5:50069400-50072000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:50069400-50073400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:50069400-50084200	Weak transcription	Liver	Liver
41	chr5:50069600-50070400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:50069600-50071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:50069600-50071000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr5:50069600-50071000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:50069600-50071200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:50069600-50071400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:50069600-50071600	Weak transcription	Primary B cells from cord blood	blood
48	chr5:50069600-50072600	Weak transcription	Primary T cells from cord blood	blood
49	chr5:50069600-50072600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:50069600-50072600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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