Variant report

Variant	rs2972369
Chromosome Location	chr5:68543295-68543296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10805428	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1134774	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11739602	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12188270	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12520485	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13161541	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13163459	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13178023	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13182409	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1976101	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2054974	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054975	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054976	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130756	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2172055	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2327638	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327639	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932785	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932787	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932788	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932789	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932790	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932793	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972357	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972364	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972367	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972379	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972384	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972385	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34261117	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34449359	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34591347	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34657177	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350092	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350096	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350118	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs350121	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4367248	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4423955	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs668139	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6865178	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71622283	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7706902	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711657	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1795469	chr5:68534233-68565285	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2972369	RAD17	cis	Muscle Skeletal	GTEx
rs2972369	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:68531600-68554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:68531800-68545800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:68531800-68552200	Weak transcription	Colonic Mucosa	Colon
6	chr5:68531800-68552200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:68531800-68554600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:68531800-68556000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:68531800-68556800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:68532200-68551400	Weak transcription	Psoas Muscle	Psoas
11	chr5:68532200-68553400	Weak transcription	Fetal Heart	heart
12	chr5:68532400-68551600	Weak transcription	Ovary	ovary
13	chr5:68532400-68558600	Weak transcription	Brain Substantia Nigra	brain
14	chr5:68532400-68558800	Weak transcription	Brain Angular Gyrus	brain
15	chr5:68532400-68563600	Weak transcription	Fetal Brain Male	brain
16	chr5:68532400-68574600	Weak transcription	Spleen	Spleen
17	chr5:68533200-68545800	Weak transcription	Adipose Nuclei	Adipose
18	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:68533400-68551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:68533600-68546200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:68533600-68552200	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:68533600-68552400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:68533800-68544200	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:68534200-68552400	Weak transcription	Fetal Brain Female	brain
25	chr5:68534400-68546200	Weak transcription	Lung	lung
26	chr5:68534400-68552000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:68534400-68554600	Weak transcription	Gastric	stomach
28	chr5:68534400-68556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:68534400-68575200	Weak transcription	Aorta	Aorta
30	chr5:68534800-68546000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:68534800-68546200	Weak transcription	Esophagus	oesophagus
32	chr5:68534800-68546200	Weak transcription	Thymus	Thymus
33	chr5:68534800-68551800	Weak transcription	Left Ventricle	heart
34	chr5:68534800-68554200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:68535000-68551600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr5:68535200-68550800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr5:68535200-68558800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr5:68535200-68559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:68535400-68546400	Weak transcription	Pancreas	Pancrea
40	chr5:68535400-68551600	Weak transcription	HUVEC	blood vessel
41	chr5:68535400-68553400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:68535400-68553400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:68535400-68556600	Weak transcription	HSMMtube	muscle
44	chr5:68535600-68552400	Weak transcription	Fetal Kidney	kidney
45	chr5:68535800-68546000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:68536000-68550600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:68536200-68548400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:68536400-68543400	Weak transcription	Primary T cells from cord blood	blood
49	chr5:68536400-68546000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:68536400-68550800	Weak transcription	Primary B cells from peripheral blood	blood

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