Variant report

Variant	rs10139000
Chromosome Location	chr14:55849876-55849877
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55839764..55841295-chr14:55849699..55852190,2	MCF-7	breast:
2	chr14:55847857..55850141-chr14:56058173..56060941,2	MCF-7	breast:
3	chr14:55845918..55850716-chr14:55877074..55879382,5	K562	blood:
4	chr14:55842441..55844954-chr14:55847953..55850798,4	K562	blood:

Variant related genes	Relation type
ENSG00000126775	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10129505	0.82[ASN][1000 genomes]
rs10131562	0.98[ASN][1000 genomes]
rs10131730	0.97[ASN][1000 genomes]
rs10131913	0.83[EUR][1000 genomes]
rs10132453	0.97[ASN][1000 genomes]
rs10134317	0.83[ASN][1000 genomes]
rs10136596	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10137307	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10139083	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10140869	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10141396	0.96[ASN][1000 genomes]
rs10141483	0.83[EUR][1000 genomes]
rs10141552	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10142448	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10142547	0.81[EUR][1000 genomes]
rs10144345	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10144418	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10145203	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10147765	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10149420	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10150760	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045002	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1109170	0.84[EUR][1000 genomes]
rs11158034	0.81[ASN][1000 genomes]
rs11158037	0.98[ASN][1000 genomes]
rs11625001	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11625423	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11625968	0.91[EUR][1000 genomes]
rs11626751	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11628437	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11851169	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050099	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12050123	0.96[ASN][1000 genomes]
rs1572611	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17128440	0.96[EUR][1000 genomes]
rs17674463	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17674563	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17675223	0.84[ASN][1000 genomes]
rs17740551	0.81[ASN][1000 genomes]
rs17740741	0.84[ASN][1000 genomes]
rs17741542	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17741831	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1815580	0.91[EUR][1000 genomes]
rs1815581	0.93[EUR][1000 genomes]
rs1972221	0.82[ASN][1000 genomes]
rs2009291	0.95[EUR][1000 genomes]
rs2016931	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026633	0.81[ASN][1000 genomes]
rs2182797	0.93[EUR][1000 genomes]
rs2209808	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297816	0.98[ASN][1000 genomes]
rs28428911	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28430823	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28452705	0.98[ASN][1000 genomes]
rs28493647	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28504448	0.87[AMR][1000 genomes]
rs28568813	0.85[EUR][1000 genomes]
rs28612464	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28631821	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28660594	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716725	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35112084	0.82[ASN][1000 genomes]
rs3742569	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3783648	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783649	0.97[ASN][1000 genomes]
rs3783650	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3783651	0.98[ASN][1000 genomes]
rs3783652	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825616	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4366639	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4496026	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4580079	0.82[ASN][1000 genomes]
rs4597235	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56270323	0.93[EUR][1000 genomes]
rs56949365	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58260073	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58296156	0.97[ASN][1000 genomes]
rs59629906	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59871474	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60248556	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61210954	0.81[EUR][1000 genomes]
rs6573017	0.95[EUR][1000 genomes]
rs6573020	0.97[EUR][1000 genomes]
rs66464079	0.82[ASN][1000 genomes]
rs66486619	0.95[EUR][1000 genomes]
rs66551709	0.83[ASN][1000 genomes]
rs66696758	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67386901	0.81[ASN][1000 genomes]
rs67412516	0.98[ASN][1000 genomes]
rs67514154	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67795323	0.83[ASN][1000 genomes]
rs68046603	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68138420	0.82[ASN][1000 genomes]
rs7140628	0.82[ASN][1000 genomes]
rs7144737	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145727	0.87[EUR][1000 genomes]
rs7147136	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7147247	0.82[ASN][1000 genomes]
rs7148171	0.81[EUR][1000 genomes]
rs7150234	0.91[ASN][1000 genomes]
rs7150763	0.98[ASN][1000 genomes]
rs7151581	0.81[ASN][1000 genomes]
rs7151754	0.81[ASN][1000 genomes]
rs7152390	0.95[ASN][1000 genomes]
rs7153110	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7153612	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7153645	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7154796	0.83[ASN][1000 genomes]
rs7154831	0.97[ASN][1000 genomes]
rs7154889	0.96[EUR][1000 genomes]
rs7155954	0.81[ASN][1000 genomes]
rs7157308	0.81[ASN][1000 genomes]
rs7158768	0.81[EUR][1000 genomes]
rs7158791	0.97[ASN][1000 genomes]
rs7158861	0.81[ASN][1000 genomes]
rs7159144	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7159824	0.82[ASN][1000 genomes]
rs7161439	0.98[ASN][1000 genomes]
rs72715769	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717738	0.98[ASN][1000 genomes]
rs73263927	0.81[ASN][1000 genomes]
rs8005450	0.91[ASN][1000 genomes]
rs8006525	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8008119	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8013713	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8014477	0.98[ASN][1000 genomes]
rs8014540	0.98[ASN][1000 genomes]
rs8015211	0.98[ASN][1000 genomes]
rs8021583	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8022041	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9323284	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9323285	0.84[ASN][1000 genomes]
rs946059	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9919923	0.96[ASN][1000 genomes]
rs9919926	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9919932	0.96[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	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
2	nsv901957	chr14:55819219-55853724	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10139000	RP11-665C16.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55808800-55865200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:55814400-55853200	Weak transcription	Right Atrium	heart
3	chr14:55818200-55877600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:55818400-55858800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:55819400-55850600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:55819400-55855200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr14:55821400-55865200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr14:55831000-55859400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:55831800-55858000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr14:55832000-55850800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:55832400-55857800	Strong transcription	Liver	Liver
12	chr14:55836800-55877800	Weak transcription	Esophagus	oesophagus
13	chr14:55838200-55850400	Weak transcription	Stomach Mucosa	stomach
14	chr14:55838600-55853600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:55839400-55859200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr14:55839600-55858600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr14:55840200-55858800	Strong transcription	Primary B cells from cord blood	blood
18	chr14:55840400-55856600	Strong transcription	Fetal Intestine Large	intestine
19	chr14:55840400-55856800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:55840600-55851800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr14:55840600-55854200	Strong transcription	Brain Cingulate Gyrus	brain
22	chr14:55841000-55859000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr14:55841800-55855000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr14:55842000-55850600	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr14:55842000-55856200	Strong transcription	Fetal Muscle Leg	muscle
26	chr14:55842200-55852400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr14:55842200-55856400	Strong transcription	Placenta	Placenta
28	chr14:55842400-55852000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr14:55842400-55852400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr14:55842400-55852600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr14:55842400-55854200	Strong transcription	Brain Hippocampus Middle	brain
32	chr14:55842400-55855400	Strong transcription	Fetal Stomach	stomach
33	chr14:55842600-55852600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr14:55842600-55853400	Strong transcription	Lung	lung
35	chr14:55842800-55850000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr14:55842800-55850800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr14:55842800-55850800	Strong transcription	Rectal Smooth Muscle	rectum
38	chr14:55842800-55851400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr14:55842800-55852200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr14:55842800-55853200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr14:55843000-55850200	Strong transcription	Brain Anterior Caudate	brain
42	chr14:55843000-55852400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr14:55843200-55852600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr14:55843400-55853400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr14:55843600-55855000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr14:55844000-55854800	Weak transcription	Fetal Brain Male	brain
47	chr14:55845000-55855200	Strong transcription	Fetal Intestine Small	intestine
48	chr14:55845400-55851000	Strong transcription	Pancreas	Pancrea
49	chr14:55846000-55854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr14:55846600-55850200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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