Variant report

Variant	rs62373187
Chromosome Location	chr5:68615604-68615605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10035835	0.85[AFR][1000 genomes]
rs10038816	0.85[AFR][1000 genomes]
rs10044508	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10045361	0.80[EUR][1000 genomes]
rs10045526	0.88[ASN][1000 genomes]
rs10064264	0.85[AFR][1000 genomes]
rs10068576	0.85[AFR][1000 genomes]
rs10077458	0.85[AFR][1000 genomes]
rs10078100	0.85[AFR][1000 genomes]
rs10471350	0.82[EUR][1000 genomes]
rs10471774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10471775	0.82[EUR][1000 genomes]
rs10471776	0.81[EUR][1000 genomes]
rs10940212	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10940214	0.85[EUR][1000 genomes]
rs10940216	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10940218	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1168409	0.85[AFR][1000 genomes]
rs11748974	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1177556	0.85[AFR][1000 genomes]
rs12187268	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12188076	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12513817	0.82[ASN][1000 genomes]
rs12517724	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13362324	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1530290	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2561172	0.85[AFR][1000 genomes]
rs2561186	0.85[AFR][1000 genomes]
rs28580747	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs299088	0.85[AFR][1000 genomes]
rs299091	0.85[AFR][1000 genomes]
rs299098	0.85[AFR][1000 genomes]
rs299099	0.85[AFR][1000 genomes]
rs299102	0.85[AFR][1000 genomes]
rs34935424	0.87[EUR][1000 genomes]
rs3890705	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4252228	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4266362	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4473723	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4629549	0.81[EUR][1000 genomes]
rs4976160	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4976189	0.87[EUR][1000 genomes]
rs4976190	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4976194	0.83[EUR][1000 genomes]
rs58772585	0.84[EUR][1000 genomes]
rs60299793	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62373181	0.85[ASN][1000 genomes]
rs6450029	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6450032	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6866993	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6873869	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6875069	0.83[EUR][1000 genomes]
rs6879078	0.82[EUR][1000 genomes]
rs7708429	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7712318	0.96[AFR][1000 genomes]
rs7733556	0.81[EUR][1000 genomes]
rs9291947	0.82[EUR][1000 genomes]
rs9291948	0.82[EUR][1000 genomes]
rs9791036	0.83[AMR][1000 genomes];0.85[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	nsv969960	chr5:68613678-68646127	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62373187	CCDC125	cis	lung	GTEx
rs62373187	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs62373187	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
2	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
4	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
6	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
7	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:68577600-68627400	Weak transcription	NHEK	skin
9	chr5:68577800-68626600	Weak transcription	A549	lung
10	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:68581800-68617800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
13	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
14	chr5:68582800-68622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:68588600-68615800	Weak transcription	Colonic Mucosa	Colon
16	chr5:68591600-68627600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:68596000-68626800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:68599600-68627800	Weak transcription	NH-A	brain
19	chr5:68601400-68627600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:68605600-68627400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:68606200-68625600	Weak transcription	Hela-S3	cervix
22	chr5:68609400-68622400	Weak transcription	K562	blood
23	chr5:68609600-68624000	Weak transcription	Placenta	Placenta
24	chr5:68609600-68627400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr5:68609600-68627600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:68609800-68615800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:68609800-68616000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr5:68609800-68617600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:68609800-68621000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:68609800-68621000	Weak transcription	Thymus	Thymus
31	chr5:68609800-68627200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:68609800-68627400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:68609800-68627400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:68609800-68627400	Weak transcription	Esophagus	oesophagus
35	chr5:68609800-68627400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:68609800-68627400	Weak transcription	GM12878-XiMat	blood
37	chr5:68609800-68627600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:68609800-68627600	Weak transcription	Fetal Thymus	thymus
39	chr5:68609800-68628200	Weak transcription	Right Ventricle	heart
40	chr5:68609800-68628400	Weak transcription	Lung	lung
41	chr5:68610000-68616000	Weak transcription	Left Ventricle	heart
42	chr5:68610000-68616000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr5:68610000-68619600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr5:68610000-68620200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr5:68610000-68621200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:68610000-68623600	Weak transcription	Fetal Intestine Large	intestine
47	chr5:68610000-68627400	Weak transcription	Dnd41	blood
48	chr5:68610400-68627600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr5:68610600-68616000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr5:68610600-68621600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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