Variant report

Variant	rs10139083
Chromosome Location	chr14:55782735-55782736
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55775205..55778244-chr14:55782229..55785495,4	MCF-7	breast:
2	chr14:55735907..55739528-chr14:55781746..55784887,4	MCF-7	breast:
3	chr14:55775251..55779667-chr14:55780270..55783872,4	K562	blood:

Variant related genes	Relation type
ENSG00000258413	Chromatin interaction
ENSG00000178974	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10129505	0.98[ASN][1000 genomes]
rs10131562	0.81[ASN][1000 genomes]
rs10131730	0.83[ASN][1000 genomes]
rs10131913	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10131926	0.88[EUR][1000 genomes]
rs10132453	0.83[ASN][1000 genomes]
rs10134317	0.95[ASN][1000 genomes]
rs10136596	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10137307	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10139000	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10139337	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10139678	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10139683	0.89[ASN][1000 genomes]
rs10140063	0.84[ASN][1000 genomes]
rs10140801	0.89[EUR][1000 genomes]
rs10140869	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10141396	0.82[ASN][1000 genomes]
rs10141483	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10141552	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10142448	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10142547	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10142803	0.94[ASN][1000 genomes]
rs10142823	0.91[EUR][1000 genomes]
rs10143136	0.95[ASN][1000 genomes]
rs10144345	0.82[EUR][1000 genomes]
rs10144418	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10145203	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10146637	0.95[ASN][1000 genomes]
rs10147765	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10149420	0.82[EUR][1000 genomes]
rs10150699	0.91[EUR][1000 genomes]
rs10150760	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1045002	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10467798	0.90[EUR][1000 genomes]
rs1109170	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11158034	0.96[ASN][1000 genomes]
rs11158037	0.82[ASN][1000 genomes]
rs11547116	0.92[EUR][1000 genomes]
rs11625001	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11625423	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11626751	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11628437	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11848456	0.95[ASN][1000 genomes]
rs11848575	0.95[ASN][1000 genomes]
rs11851169	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12050099	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050123	0.82[ASN][1000 genomes]
rs13379169	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1572611	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17128440	0.82[EUR][1000 genomes]
rs17674463	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17674563	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17740551	0.96[ASN][1000 genomes]
rs17740741	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17741542	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17741831	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1952087	0.86[EUR][1000 genomes]
rs1972221	0.98[ASN][1000 genomes]
rs2009291	0.81[EUR][1000 genomes]
rs2016931	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2026633	0.98[ASN][1000 genomes]
rs2209808	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2297816	0.82[ASN][1000 genomes]
rs2341621	0.91[EUR][1000 genomes]
rs2341622	0.91[EUR][1000 genomes]
rs28428911	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28430823	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28452705	0.81[ASN][1000 genomes]
rs28493647	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28504448	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28568813	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28612464	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28631821	0.82[EUR][1000 genomes]
rs28660594	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28716725	0.82[EUR][1000 genomes]
rs2880103	0.89[ASN][1000 genomes]
rs35112084	0.98[ASN][1000 genomes]
rs3742569	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3783648	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3783649	0.81[ASN][1000 genomes]
rs3783650	0.82[EUR][1000 genomes]
rs3783651	0.81[ASN][1000 genomes]
rs3783652	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3825616	0.81[EUR][1000 genomes]
rs4366639	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4496026	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4580079	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4597235	0.82[EUR][1000 genomes]
rs56166765	0.84[ASN][1000 genomes]
rs56949365	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58260073	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58296156	0.83[ASN][1000 genomes]
rs58458194	0.94[ASN][1000 genomes]
rs59629906	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59871474	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60248556	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61210954	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6573009	0.86[EUR][1000 genomes]
rs6573010	0.88[EUR][1000 genomes]
rs6573014	0.92[EUR][1000 genomes]
rs6573017	0.81[EUR][1000 genomes]
rs6573020	0.82[EUR][1000 genomes]
rs66464079	0.96[ASN][1000 genomes]
rs66486619	0.81[EUR][1000 genomes]
rs66551709	0.95[ASN][1000 genomes]
rs66696758	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67386901	0.95[ASN][1000 genomes]
rs67412516	0.81[ASN][1000 genomes]
rs67514154	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67795323	0.95[ASN][1000 genomes]
rs67822108	0.95[ASN][1000 genomes]
rs68046603	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68138420	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7140628	0.96[ASN][1000 genomes]
rs7142857	0.87[EUR][1000 genomes]
rs7144292	0.85[EUR][1000 genomes]
rs7144737	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7146748	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7146752	0.92[EUR][1000 genomes]
rs7147136	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7147247	0.98[ASN][1000 genomes]
rs7148171	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7150234	0.87[ASN][1000 genomes]
rs7150763	0.82[ASN][1000 genomes]
rs7151581	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7151754	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7152390	0.83[ASN][1000 genomes]
rs7153110	0.81[EUR][1000 genomes]
rs7153612	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153645	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7154796	0.97[ASN][1000 genomes]
rs7154831	0.83[ASN][1000 genomes]
rs7154889	0.82[EUR][1000 genomes]
rs7155954	0.96[ASN][1000 genomes]
rs7157308	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7158768	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7158791	0.83[ASN][1000 genomes]
rs7158861	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7159144	0.81[EUR][1000 genomes]
rs7159824	0.96[ASN][1000 genomes]
rs7161439	0.81[ASN][1000 genomes]
rs72715769	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72717738	0.81[ASN][1000 genomes]
rs73263927	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs8005450	0.87[ASN][1000 genomes]
rs8006525	0.81[EUR][1000 genomes]
rs8008119	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8011288	0.90[EUR][1000 genomes]
rs8013713	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8014477	0.82[ASN][1000 genomes]
rs8014540	0.82[ASN][1000 genomes]
rs8015211	0.82[ASN][1000 genomes]
rs8021583	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8022041	0.80[EUR][1000 genomes]
rs8022225	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9323284	0.82[EUR][1000 genomes]
rs943590	0.93[EUR][1000 genomes]
rs946059	0.82[EUR][1000 genomes]
rs9919923	0.82[ASN][1000 genomes]
rs9919926	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9919932	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10139083	RP11-665C16.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55768600-55783800	Weak transcription	Right Ventricle	heart
2	chr14:55768800-55786400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr14:55770800-55783800	Weak transcription	Fetal Kidney	kidney
4	chr14:55773600-55783000	Weak transcription	Pancreas	Pancrea
5	chr14:55775000-55783000	Weak transcription	Left Ventricle	heart
6	chr14:55776600-55786600	Weak transcription	Fetal Brain Male	brain
7	chr14:55777000-55792800	Weak transcription	Brain Angular Gyrus	brain
8	chr14:55777000-55795000	Weak transcription	NHDF-Ad	bronchial
9	chr14:55777200-55783800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr14:55777200-55799000	Weak transcription	Colon Smooth Muscle	Colon
11	chr14:55777400-55795000	Weak transcription	Osteobl	bone
12	chr14:55777400-55799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr14:55778200-55785200	Weak transcription	Small Intestine	intestine
14	chr14:55779200-55793800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr14:55779200-55798800	Weak transcription	K562	blood
16	chr14:55779200-55817600	Weak transcription	Hela-S3	cervix
17	chr14:55779400-55783800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:55779600-55783000	Weak transcription	Fetal Stomach	stomach
19	chr14:55779600-55783600	Weak transcription	Gastric	stomach
20	chr14:55779600-55783800	Weak transcription	Colonic Mucosa	Colon
21	chr14:55779600-55784400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr14:55779600-55789200	Weak transcription	HUVEC	blood vessel
23	chr14:55779600-55795200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr14:55779600-55796800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:55779600-55796800	Weak transcription	Ovary	ovary
26	chr14:55779600-55797200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr14:55779600-55799600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr14:55779600-55801200	Weak transcription	Esophagus	oesophagus
29	chr14:55779800-55787200	Weak transcription	Placenta	Placenta
30	chr14:55779800-55794400	Weak transcription	HepG2	liver
31	chr14:55779800-55794800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr14:55779800-55795400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr14:55779800-55800800	Weak transcription	Adipose Nuclei	Adipose
34	chr14:55780000-55783000	Weak transcription	HSMMtube	muscle
35	chr14:55780000-55797200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr14:55780000-55797800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr14:55780200-55783200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr14:55780200-55785600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:55780200-55790000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr14:55780200-55792600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr14:55780200-55793600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr14:55780200-55807800	Weak transcription	Thymus	Thymus
43	chr14:55780400-55790400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr14:55780400-55793600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr14:55780600-55783400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr14:55780600-55783400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr14:55780600-55787600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr14:55780600-55789200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr14:55780600-55792600	Weak transcription	Brain Hippocampus Middle	brain
50	chr14:55780600-55795200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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