Variant report

Variant	rs12189395
Chromosome Location	chr5:68522298-68522299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68511483..68514231-chr5:68521501..68524879,3	K562	blood:
2	chr5:68521905..68524098-chr5:68627752..68629911,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134056	Chromatin interaction
ENSG00000183323	Chromatin interaction
ENSG00000215006	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10454825	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10515100	0.83[ASN][1000 genomes]
rs10940208	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1128761	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12188874	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16875380	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17271735	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17271763	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17271912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17331590	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069432	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28616082	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3846484	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3966728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41392244	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56072942	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56101109	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56667192	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57047253	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58176819	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58725071	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59497209	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61626775	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61699334	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61743885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66525615	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66595384	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67275234	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67548500	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67693452	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67821207	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67980996	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6867050	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890817	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767813	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767820	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767822	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767833	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72767837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767855	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767860	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767861	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767863	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767864	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767865	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7709090	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7714908	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7734513	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7736312	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12189395	CCDC125	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68514200-68530200	Weak transcription	Small Intestine	intestine
2	chr5:68514200-68530200	Weak transcription	Spleen	Spleen
3	chr5:68514400-68523000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:68514400-68523600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:68514400-68530200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:68514400-68530200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:68514400-68530200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:68514400-68530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:68514400-68530200	Weak transcription	Aorta	Aorta
10	chr5:68514400-68530200	Weak transcription	Esophagus	oesophagus
11	chr5:68514400-68530200	Weak transcription	Gastric	stomach
12	chr5:68514400-68530200	Weak transcription	Pancreas	Pancrea
13	chr5:68514400-68530200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:68514600-68523000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:68514600-68523400	Weak transcription	HSMM	muscle
16	chr5:68514600-68523600	Weak transcription	Ovary	ovary
17	chr5:68514600-68524000	Weak transcription	HSMMtube	muscle
18	chr5:68514800-68523000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:68514800-68523400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:68514800-68523400	Weak transcription	Osteobl	bone
21	chr5:68514800-68523600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:68514800-68524000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:68514800-68524000	Weak transcription	NH-A	brain
24	chr5:68514800-68524200	Weak transcription	HUVEC	blood vessel
25	chr5:68514800-68530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:68515000-68523000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:68515000-68523400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:68515000-68524000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:68515000-68524200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:68515000-68530000	Weak transcription	Psoas Muscle	Psoas
31	chr5:68515200-68522800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:68515200-68523000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr5:68515200-68523000	Weak transcription	A549	lung
34	chr5:68515200-68523400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:68515200-68523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:68515200-68523400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:68515200-68523400	Weak transcription	Adipose Nuclei	Adipose
38	chr5:68515200-68523400	Weak transcription	NHEK	skin
39	chr5:68515200-68523600	Weak transcription	Primary T cells from cord blood	blood
40	chr5:68515200-68523600	Weak transcription	HMEC	breast
41	chr5:68515200-68524000	Weak transcription	Brain Germinal Matrix	brain
42	chr5:68515200-68524000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:68515200-68529800	Weak transcription	Fetal Brain Female	brain
44	chr5:68515200-68529800	Weak transcription	NHLF	lung
45	chr5:68515200-68530000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr5:68515200-68530000	Weak transcription	Fetal Brain Male	brain
47	chr5:68515200-68530000	Weak transcription	Fetal Kidney	kidney
48	chr5:68515200-68530000	Weak transcription	Fetal Lung	lung
49	chr5:68515400-68522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:68515400-68522800	Weak transcription	Rectal Mucosa Donor 29	rectum

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