Variant report

Variant	rs2972384
Chromosome Location	chr5:68537273-68537274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68534182..68537947-chr5:68660840..68664102,4	K562	blood:
2	chr5:68536149..68538445-chr5:68627024..68629643,2	MCF-7	breast:
3	chr5:68533315..68535936-chr5:68536358..68538976,2	K562	blood:

Variant related genes	Relation type
ENSG00000085231	Chromatin interaction
ENSG00000183323	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10805428	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1134774	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11739602	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12188270	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12520485	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13161541	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13163459	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13178023	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13182409	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1976101	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2054974	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054975	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054976	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2130756	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172055	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2327638	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2327639	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28499200	0.81[ASN][1000 genomes]
rs2932785	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932787	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932788	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932789	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932790	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932793	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972357	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972364	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972367	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972369	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972379	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972385	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34261117	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34449359	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34591347	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34657177	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350092	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350096	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350118	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350121	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4367248	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4423955	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs668139	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6865178	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71622283	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7706902	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711657	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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
rs2972384	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2972384	RAD17	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 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	chr5:68531400-68537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:68531600-68554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:68531800-68538800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:68531800-68545800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:68531800-68552200	Weak transcription	Colonic Mucosa	Colon
8	chr5:68531800-68552200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:68531800-68554600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:68531800-68556000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:68531800-68556800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:68532200-68551400	Weak transcription	Psoas Muscle	Psoas
13	chr5:68532200-68553400	Weak transcription	Fetal Heart	heart
14	chr5:68532400-68539600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:68532400-68551600	Weak transcription	Ovary	ovary
16	chr5:68532400-68558600	Weak transcription	Brain Substantia Nigra	brain
17	chr5:68532400-68558800	Weak transcription	Brain Angular Gyrus	brain
18	chr5:68532400-68563600	Weak transcription	Fetal Brain Male	brain
19	chr5:68532400-68574600	Weak transcription	Spleen	Spleen
20	chr5:68532800-68540800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:68533000-68538400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:68533000-68539200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:68533200-68538000	Strong transcription	Fetal Thymus	thymus
24	chr5:68533200-68538400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:68533200-68539200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr5:68533200-68545800	Weak transcription	Adipose Nuclei	Adipose
27	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr5:68533400-68538600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:68533400-68551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:68533600-68538600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:68533600-68546200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:68533600-68552200	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:68533600-68552400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:68533800-68538000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:68533800-68538200	Strong transcription	Fetal Intestine Large	intestine
36	chr5:68533800-68538800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr5:68533800-68544200	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:68534000-68539800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:68534200-68552400	Weak transcription	Fetal Brain Female	brain
40	chr5:68534400-68546200	Weak transcription	Lung	lung
41	chr5:68534400-68552000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:68534400-68554600	Weak transcription	Gastric	stomach
43	chr5:68534400-68556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:68534400-68575200	Weak transcription	Aorta	Aorta
45	chr5:68534800-68538000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:68534800-68546000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:68534800-68546200	Weak transcription	Esophagus	oesophagus
48	chr5:68534800-68546200	Weak transcription	Thymus	Thymus
49	chr5:68534800-68551800	Weak transcription	Left Ventricle	heart
50	chr5:68534800-68554200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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