Variant report

Variant	rs68083627
Chromosome Location	chr5:68596899-68596900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68594908..68597082-chr5:68664416..68666422,2	K562	blood:
2	chr5:68595037..68597280-chr5:68662631..68665020,2	K562	blood:
3	chr11:76631123..76631684-chr5:68596557..68597057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152942	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10940215	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11741775	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11741826	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11742878	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11745537	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11745591	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11749723	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11750525	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11957698	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12189282	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13154469	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13168973	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28499200	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34449757	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34862981	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35316810	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35438259	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4288083	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62373182	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66514959	0.80[EUR][1000 genomes]
rs6865481	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6869305	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6877725	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6881767	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6893648	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72767881	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs68083627	CCDC125	cis	lung	GTEx
rs68083627	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs68083627	CCDC125	cis	Thyroid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
3	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
5	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:68575600-68605000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:68575600-68608200	Weak transcription	Right Ventricle	heart
9	chr5:68576000-68605200	Weak transcription	Left Ventricle	heart
10	chr5:68576200-68605200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:68576200-68609400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
14	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
16	chr5:68577200-68601400	Weak transcription	Aorta	Aorta
17	chr5:68577400-68605200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:68577400-68607800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
20	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:68577600-68627400	Weak transcription	NHEK	skin
22	chr5:68577800-68626600	Weak transcription	A549	lung
23	chr5:68579000-68603600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:68581600-68601200	Weak transcription	Fetal Thymus	thymus
25	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:68581800-68605200	Weak transcription	GM12878-XiMat	blood
27	chr5:68581800-68608200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:68581800-68609000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:68581800-68609200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:68581800-68611000	Weak transcription	Psoas Muscle	Psoas
31	chr5:68581800-68617800	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
33	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
34	chr5:68582000-68601600	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:68582800-68622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:68585000-68609000	Weak transcription	Spleen	Spleen
37	chr5:68587200-68602400	Strong transcription	Fetal Intestine Small	intestine
38	chr5:68587600-68597800	Strong transcription	Liver	Liver
39	chr5:68587800-68597800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:68588600-68615800	Weak transcription	Colonic Mucosa	Colon
41	chr5:68588800-68605000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:68589200-68605000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:68590800-68605200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:68591200-68606200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr5:68591400-68600600	Weak transcription	Dnd41	blood
46	chr5:68591400-68603400	Weak transcription	Ovary	ovary
47	chr5:68591400-68605000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:68591400-68605200	Weak transcription	Thymus	Thymus
49	chr5:68591400-68606200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:68591600-68609200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links