Variant report

Variant	rs4976190
Chromosome Location	chr5:68612121-68612122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs100192	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10044508	0.83[EUR][1000 genomes]
rs10045361	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10471350	0.86[EUR][1000 genomes]
rs10471774	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10471775	0.86[EUR][1000 genomes]
rs10471776	0.85[EUR][1000 genomes]
rs10940210	0.80[ASN][1000 genomes]
rs10940212	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10940214	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10940216	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940218	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11748974	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12187268	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12188076	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12517724	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13175606	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1530290	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs163443	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs163444	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs164386	0.82[CHB][hapmap]
rs164390	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2450246	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs28580747	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2930945	0.80[ASN][1000 genomes]
rs2932772	0.81[ASN][1000 genomes]
rs2932773	0.81[ASN][1000 genomes]
rs2932775	0.81[ASN][1000 genomes]
rs2932776	0.81[ASN][1000 genomes]
rs34935424	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350107	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs350123	0.81[ASN][1000 genomes]
rs351424	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs352626	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs389686	0.80[JPT][hapmap]
rs3934528	0.80[ASN][1000 genomes]
rs4077460	0.80[ASN][1000 genomes]
rs4266362	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4362903	0.80[ASN][1000 genomes]
rs4421064	0.80[ASN][1000 genomes]
rs444305	0.82[CHB][hapmap]
rs4473723	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4629549	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4976160	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4976189	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4976194	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58772585	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60299793	0.88[EUR][1000 genomes]
rs62373164	0.80[ASN][1000 genomes]
rs62373187	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6450029	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6450032	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs648489	0.82[CHB][hapmap]
rs651076	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs6866993	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873869	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875069	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6876783	0.80[ASN][1000 genomes]
rs6879078	0.86[EUR][1000 genomes]
rs693725	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7708429	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7733556	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs875459	0.81[CHB][hapmap]
rs9291947	0.86[EUR][1000 genomes]
rs9291948	0.86[EUR][1000 genomes]
rs9791036	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4976190	CCDC125	cis	Thyroid	GTEx
rs4976190	CCDC125	cis	lung	GTEx
rs4976190	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs4976190	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:78 , 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	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
5	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
7	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
8	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:68577600-68627400	Weak transcription	NHEK	skin
10	chr5:68577800-68626600	Weak transcription	A549	lung
11	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:68581800-68617800	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
14	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
15	chr5:68582800-68622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:68588600-68615800	Weak transcription	Colonic Mucosa	Colon
17	chr5:68591600-68614000	Weak transcription	Osteobl	bone
18	chr5:68591600-68627600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:68596000-68626800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:68596600-68612800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:68599600-68627800	Weak transcription	NH-A	brain
22	chr5:68601400-68627600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:68605600-68613800	Weak transcription	Brain Germinal Matrix	brain
24	chr5:68605600-68627400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:68606200-68625600	Weak transcription	Hela-S3	cervix
26	chr5:68607400-68612600	Strong transcription	Fetal Intestine Small	intestine
27	chr5:68608400-68613200	Weak transcription	Primary B cells from cord blood	blood
28	chr5:68609000-68612800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:68609000-68613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:68609400-68622400	Weak transcription	K562	blood
31	chr5:68609600-68613400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr5:68609600-68624000	Weak transcription	Placenta	Placenta
33	chr5:68609600-68627400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:68609600-68627600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:68609800-68613800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:68609800-68615200	Weak transcription	Gastric	stomach
37	chr5:68609800-68615800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:68609800-68616000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:68609800-68617600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:68609800-68621000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:68609800-68621000	Weak transcription	Thymus	Thymus
42	chr5:68609800-68627200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr5:68609800-68627400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:68609800-68627400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:68609800-68627400	Weak transcription	Esophagus	oesophagus
46	chr5:68609800-68627400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr5:68609800-68627400	Weak transcription	GM12878-XiMat	blood
48	chr5:68609800-68627600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr5:68609800-68627600	Weak transcription	Fetal Thymus	thymus
50	chr5:68609800-68628200	Weak transcription	Right Ventricle	heart

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