Variant report

Variant	rs2972386
Chromosome Location	chr5:68532976-68532977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68389043..68391533-chr5:68531972..68533931,2	K562	blood:
2	chr5:68512355..68516868-chr5:68528060..68533660,10	K562	blood:

Variant related genes	Relation type
ENSG00000145740	Chromatin interaction
ENSG00000134056	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10063757	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10940209	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940210	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940212	0.82[ASN][1000 genomes]
rs10940216	0.82[ASN][1000 genomes]
rs11744596	0.81[ASN][1000 genomes]
rs11748974	0.89[ASN][1000 genomes]
rs12659146	0.81[ASN][1000 genomes]
rs13175606	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs151589	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs163444	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164709	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs164715	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164789	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1650779	0.87[ASN][1000 genomes]
rs171212	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs184747	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976103	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2002825	0.81[ASN][1000 genomes]
rs2130757	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171148	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172056	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242350	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2242351	0.81[ASN][1000 genomes]
rs2291519	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291520	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450230	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2450246	0.85[ASN][1000 genomes]
rs2637128	0.80[ASN][1000 genomes]
rs28602964	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28768211	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2930944	0.81[ASN][1000 genomes]
rs2930945	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930946	0.81[ASN][1000 genomes]
rs2930949	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930951	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932767	0.85[ASN][1000 genomes]
rs2932770	0.81[ASN][1000 genomes]
rs2932771	0.81[ASN][1000 genomes]
rs2932772	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932773	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932774	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2932775	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932776	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932777	0.81[ASN][1000 genomes]
rs2932778	0.82[ASN][1000 genomes]
rs2932780	0.85[ASN][1000 genomes]
rs2932782	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932783	0.85[ASN][1000 genomes]
rs2972358	0.81[ASN][1000 genomes]
rs2972361	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972366	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972373	0.81[ASN][1000 genomes]
rs2972374	0.81[ASN][1000 genomes]
rs2972377	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972378	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972381	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972387	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972388	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972390	0.81[ASN][1000 genomes]
rs34893396	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34935424	0.85[ASN][1000 genomes]
rs350104	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs350106	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs350107	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350109	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350115	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350116	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs350122	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350123	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350124	0.81[ASN][1000 genomes]
rs351424	0.89[ASN][1000 genomes]
rs35308484	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs353656	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs379106	0.89[ASN][1000 genomes]
rs386640	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3934528	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077460	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419902	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs426392	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4266362	0.91[ASN][1000 genomes]
rs4362903	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4421064	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4541612	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4629549	0.92[ASN][1000 genomes]
rs488498	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4976188	0.80[ASN][1000 genomes]
rs4976189	0.85[ASN][1000 genomes]
rs603029	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62373164	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6450026	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6450027	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6450029	0.85[ASN][1000 genomes]
rs651076	0.87[ASN][1000 genomes]
rs676012	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs676879	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6862253	0.83[ASN][1000 genomes]
rs6866993	0.92[ASN][1000 genomes]
rs6873869	0.85[ASN][1000 genomes]
rs6876783	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs693725	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7733556	0.92[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	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2972386	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2972386	GUSBP3	cis	Whole Blood	GTEx
rs2972386	CCDC125	cis	Muscle Skeletal	GTEx
rs2972386	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs2972386	CCDC125	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68529800-68533000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:68531200-68533000	Weak transcription	Lung	lung
3	chr5:68531200-68533000	Weak transcription	Pancreas	Pancrea
4	chr5:68531200-68534200	Weak transcription	Esophagus	oesophagus
5	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:68531400-68533000	Enhancers	Left Ventricle	heart
7	chr5:68531400-68533200	Weak transcription	Aorta	Aorta
8	chr5:68531400-68537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:68531600-68533800	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:68531600-68554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:68531800-68533000	Enhancers	Primary B cells from cord blood	blood
13	chr5:68531800-68533000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:68531800-68533000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:68531800-68533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:68531800-68533000	Weak transcription	Brain Germinal Matrix	brain
17	chr5:68531800-68533400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:68531800-68533400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr5:68531800-68533400	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr5:68531800-68533600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:68531800-68533600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr5:68531800-68533600	Enhancers	Liver	Liver
23	chr5:68531800-68533800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr5:68531800-68534200	Weak transcription	HSMMtube	muscle
25	chr5:68531800-68534400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:68531800-68534600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:68531800-68534600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:68531800-68534800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:68531800-68535800	Weak transcription	Right Ventricle	heart
30	chr5:68531800-68538800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr5:68531800-68545800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:68531800-68552200	Weak transcription	Colonic Mucosa	Colon
33	chr5:68531800-68552200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:68531800-68554600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr5:68531800-68556000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:68531800-68556800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:68532000-68533000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr5:68532000-68533000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:68532000-68533000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:68532000-68533000	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:68532000-68533000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:68532000-68534600	Weak transcription	Small Intestine	intestine
43	chr5:68532000-68535000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:68532200-68533000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr5:68532200-68533000	Weak transcription	Fetal Brain Female	brain
46	chr5:68532200-68533000	Weak transcription	Fetal Kidney	kidney
47	chr5:68532200-68533000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr5:68532200-68533000	Weak transcription	A549	lung
49	chr5:68532200-68533200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr5:68532200-68533200	Weak transcription	Colon Smooth Muscle	Colon

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