Variant report

Variant	rs28768211
Chromosome Location	chr5:68537032-68537033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68534182..68537947-chr5:68660840..68664102,4	K562	blood:
2	chr5:68534808..68537076-chr5:68626446..68628069,2	MCF-7	breast:
3	chr5:68536149..68538445-chr5:68627024..68629643,2	MCF-7	breast:
4	chr5:68533315..68535936-chr5:68536358..68538976,2	K562	blood:

Variant related genes	Relation type
ENSG00000183323	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10045526	0.87[ASN][1000 genomes]
rs10063757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10063969	0.95[ASN][1000 genomes]
rs10940209	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10940210	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12513817	0.93[ASN][1000 genomes]
rs13175606	0.87[EUR][1000 genomes]
rs13362324	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151589	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs163444	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs164709	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164715	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs164789	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs171211	0.94[ASN][1000 genomes]
rs171212	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs184747	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1976103	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2130757	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2171148	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2172056	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2242350	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291519	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2291520	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2450230	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28602964	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2930945	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2930949	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2930951	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932772	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2932773	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2932774	0.81[EUR][1000 genomes]
rs2932775	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2932776	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932782	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2972361	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2972366	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2972377	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2972378	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2972381	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2972386	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2972387	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2972388	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34893396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350104	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350106	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350107	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs350109	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs350115	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs350116	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs350122	0.88[EUR][1000 genomes]
rs350123	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35308484	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs353656	0.85[EUR][1000 genomes]
rs386640	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3890705	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3934528	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4077460	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs419902	0.91[EUR][1000 genomes]
rs426392	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4362903	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4421064	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4541612	0.82[EUR][1000 genomes]
rs488498	0.90[EUR][1000 genomes]
rs603029	0.88[EUR][1000 genomes]
rs62373164	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62373181	0.85[ASN][1000 genomes]
rs6450026	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450027	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676012	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676879	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6876783	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs693725	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28768211	CCDC125	cis	lung	GTEx
rs28768211	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs28768211	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:117 , 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	chr5:68531400-68537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:68531600-68554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:68531800-68538800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:68531800-68545800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:68531800-68552200	Weak transcription	Colonic Mucosa	Colon
8	chr5:68531800-68552200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:68531800-68554600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:68531800-68556000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:68531800-68556800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:68532200-68551400	Weak transcription	Psoas Muscle	Psoas
13	chr5:68532200-68553400	Weak transcription	Fetal Heart	heart
14	chr5:68532400-68537200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:68532400-68539600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:68532400-68551600	Weak transcription	Ovary	ovary
17	chr5:68532400-68558600	Weak transcription	Brain Substantia Nigra	brain
18	chr5:68532400-68558800	Weak transcription	Brain Angular Gyrus	brain
19	chr5:68532400-68563600	Weak transcription	Fetal Brain Male	brain
20	chr5:68532400-68574600	Weak transcription	Spleen	Spleen
21	chr5:68532800-68540800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:68533000-68538400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:68533000-68539200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:68533200-68538000	Strong transcription	Fetal Thymus	thymus
25	chr5:68533200-68538400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:68533200-68539200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:68533200-68545800	Weak transcription	Adipose Nuclei	Adipose
28	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:68533400-68537200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:68533400-68538600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:68533400-68551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:68533600-68538600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr5:68533600-68546200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:68533600-68552200	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:68533600-68552400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:68533800-68538000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:68533800-68538200	Strong transcription	Fetal Intestine Large	intestine
38	chr5:68533800-68538800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:68533800-68544200	Weak transcription	Fetal Muscle Leg	muscle
40	chr5:68534000-68539800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:68534200-68552400	Weak transcription	Fetal Brain Female	brain
42	chr5:68534400-68546200	Weak transcription	Lung	lung
43	chr5:68534400-68552000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:68534400-68554600	Weak transcription	Gastric	stomach
45	chr5:68534400-68556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr5:68534400-68575200	Weak transcription	Aorta	Aorta
47	chr5:68534800-68538000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:68534800-68546000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:68534800-68546200	Weak transcription	Esophagus	oesophagus
50	chr5:68534800-68546200	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links