Variant report

Variant	rs3966728
Chromosome Location	chr5:68508425-68508426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68508210..68511078-chr5:68511124..68514731,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134056	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10515100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10940208	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1128761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12188874	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12189395	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16875380	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17271735	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17271763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17271912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17331590	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28616082	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3846484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41392244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56072942	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56101109	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56667192	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57047253	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58176819	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58725071	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59497209	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61626775	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61699334	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61743885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66525615	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66595384	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67275234	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67548500	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67693452	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67821207	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67980996	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6867050	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890817	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767813	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767820	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72767837	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767849	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767855	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767860	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767861	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767863	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767864	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767865	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7709090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7714908	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7734513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7736312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[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
rs3966728	CCDC125	cis	lung	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68486000-68513600	Weak transcription	Gastric	stomach
2	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:68486200-68509400	Weak transcription	HSMM	muscle
5	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
7	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
9	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
10	chr5:68486400-68513000	Weak transcription	Osteobl	bone
11	chr5:68486600-68509200	Weak transcription	NHDF-Ad	bronchial
12	chr5:68487400-68511200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:68487600-68509000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:68490400-68513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:68492400-68513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:68492800-68512200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:68492800-68513000	Weak transcription	Fetal Brain Female	brain
18	chr5:68494200-68509400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:68494600-68513200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:68495000-68509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:68495400-68512800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:68495400-68513000	Weak transcription	HMEC	breast
23	chr5:68495400-68513400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:68495600-68509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:68495600-68512400	Weak transcription	Primary T cells from cord blood	blood
26	chr5:68495600-68512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:68495600-68512800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:68495600-68513000	Weak transcription	Fetal Lung	lung
29	chr5:68495600-68513200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:68495600-68513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:68497800-68513200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:68498000-68512800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:68498800-68509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:68500600-68513000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:68501600-68513000	Weak transcription	Thymus	Thymus
36	chr5:68502200-68509600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:68502800-68513600	Weak transcription	Small Intestine	intestine
38	chr5:68503000-68509200	Weak transcription	HepG2	liver
39	chr5:68503000-68509400	Weak transcription	A549	lung
40	chr5:68503000-68509400	Weak transcription	Hela-S3	cervix
41	chr5:68503000-68509400	Weak transcription	NHLF	lung
42	chr5:68503200-68509400	Weak transcription	NHEK	skin
43	chr5:68504200-68509000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:68505200-68509400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:68505400-68509600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:68505400-68513000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:68506400-68513000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:68506600-68509400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:68507000-68513000	Weak transcription	Fetal Stomach	stomach
50	chr5:68507000-68513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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