Variant report

Variant	rs28616082
Chromosome Location	chr5:68497853-68497854
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68483602..68486375-chr5:68497290..68499497,2	K562	blood:
2	chr5:68496257..68497924-chr5:68621428..68624082,2	K562	blood:
3	chr5:68468383..68471229-chr5:68496445..68498720,2	K562	blood:
4	chr5:68496437..68498055-chr5:68501214..68502834,2	K562	blood:

Variant related genes	Relation type
ENSG00000134057	Chromatin interaction
ENSG00000153044	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	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515100	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10940208	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1128761	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188874	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189395	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16875380	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271763	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271912	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17331590	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2069432	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3846484	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3966728	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41392244	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56072942	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101109	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56667192	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57047253	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58176819	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58725071	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59497209	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61626775	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61699334	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61743885	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66525615	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66595384	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67275234	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67548500	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67693452	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67821207	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67980996	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890817	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767813	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767816	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767820	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767822	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767833	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72767837	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767849	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767855	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767860	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767861	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767863	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767864	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767865	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7709090	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714908	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734513	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7736312	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs28616082	CCDC125	cis	lung	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68486000-68498200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:68486000-68498600	Weak transcription	Left Ventricle	heart
3	chr5:68486000-68505800	Weak transcription	Ovary	ovary
4	chr5:68486000-68513600	Weak transcription	Gastric	stomach
5	chr5:68486200-68498200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:68486200-68498400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:68486200-68499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:68486200-68499400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:68486200-68500200	Weak transcription	Thymus	Thymus
10	chr5:68486200-68502000	Weak transcription	Placenta	Placenta
11	chr5:68486200-68502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:68486200-68502600	Weak transcription	Small Intestine	intestine
13	chr5:68486200-68505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:68486200-68509400	Weak transcription	HSMM	muscle
17	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:68486400-68502400	Weak transcription	NH-A	brain
19	chr5:68486400-68502600	Weak transcription	Fetal Kidney	kidney
20	chr5:68486400-68502600	Weak transcription	HUVEC	blood vessel
21	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
22	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
24	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
25	chr5:68486400-68513000	Weak transcription	Osteobl	bone
26	chr5:68486600-68502600	Weak transcription	NHLF	lung
27	chr5:68486600-68509200	Weak transcription	NHDF-Ad	bronchial
28	chr5:68487400-68508200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:68487400-68511200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:68487600-68498000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:68487600-68500400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:68487600-68500400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:68487600-68500600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:68487600-68503000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr5:68487600-68503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:68487600-68508000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:68487600-68508000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:68487600-68508200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:68487600-68509000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:68488200-68501600	Strong transcription	Dnd41	blood
41	chr5:68488400-68502200	Weak transcription	NHEK	skin
42	chr5:68488600-68507400	Weak transcription	GM12878-XiMat	blood
43	chr5:68490400-68513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr5:68490800-68501000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:68492200-68498400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:68492200-68501200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:68492400-68500000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:68492400-68504200	Weak transcription	Fetal Intestine Small	intestine
49	chr5:68492400-68504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:68492400-68513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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