Variant report

Variant	rs10940208
Chromosome Location	chr5:68551777-68551778
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68530371..68532104-chr5:68550498..68552511,2	MCF-7	breast:
2	chr5:68549479..68552120-chr5:68553320..68555643,3	K562	blood:
3	chr5:68529657..68532330-chr5:68550673..68553166,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS36-2	chr5:68551287-68551848	NONHSAT101904

Variant related genes	Relation type
ENSG00000134058	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10454825	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1128761	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12188874	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189395	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16875380	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17271735	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17271763	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17271912	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17331590	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2069432	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28616082	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3846484	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3966728	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41392244	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56072942	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56101109	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56667192	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57047253	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58176819	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58725071	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61626775	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61743885	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66525615	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66595384	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67548500	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67693452	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67980996	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6867050	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6890817	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72767813	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72767816	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767820	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767822	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767833	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72767837	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767849	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767855	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767860	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767861	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767863	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767864	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767865	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767872	0.91[ASN][1000 genomes]
rs72767873	0.87[ASN][1000 genomes]
rs7702373	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7709090	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7714908	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7734513	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7736312	0.88[AMR][1000 genomes];0.86[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10940208	CCDC125	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	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	chr5:68531800-68552200	Weak transcription	Colonic Mucosa	Colon
5	chr5:68531800-68552200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:68531800-68554600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:68531800-68556000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:68531800-68556800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:68532200-68553400	Weak transcription	Fetal Heart	heart
10	chr5:68532400-68558600	Weak transcription	Brain Substantia Nigra	brain
11	chr5:68532400-68558800	Weak transcription	Brain Angular Gyrus	brain
12	chr5:68532400-68563600	Weak transcription	Fetal Brain Male	brain
13	chr5:68532400-68574600	Weak transcription	Spleen	Spleen
14	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:68533600-68552200	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:68533600-68552400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:68534200-68552400	Weak transcription	Fetal Brain Female	brain
18	chr5:68534400-68552000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:68534400-68554600	Weak transcription	Gastric	stomach
20	chr5:68534400-68556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:68534400-68575200	Weak transcription	Aorta	Aorta
22	chr5:68534800-68551800	Weak transcription	Left Ventricle	heart
23	chr5:68534800-68554200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:68535200-68558800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:68535200-68559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:68535400-68553400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:68535400-68553400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:68535400-68556600	Weak transcription	HSMMtube	muscle
29	chr5:68535600-68552400	Weak transcription	Fetal Kidney	kidney
30	chr5:68536400-68552600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:68536800-68553000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:68537000-68551800	Weak transcription	Dnd41	blood
33	chr5:68538400-68552000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:68538400-68552600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:68538400-68563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:68538600-68552400	Weak transcription	NH-A	brain
37	chr5:68538800-68553400	Weak transcription	NHLF	lung
38	chr5:68539000-68559200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr5:68539200-68554600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
41	chr5:68544600-68554600	Weak transcription	Brain Germinal Matrix	brain
42	chr5:68545200-68552200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:68545200-68553200	Weak transcription	Fetal Lung	lung
44	chr5:68545400-68551800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:68546000-68552400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:68546000-68553400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:68546200-68560600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:68546200-68562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr5:68546200-68579200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr5:68546400-68553400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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