Variant report

Variant	rs1025311
Chromosome Location	chr16:65017876-65017877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 152 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs1040270	0.87[JPT][hapmap]
rs1079008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445593	0.83[ASN][1000 genomes]
rs12447201	0.93[ASN][1000 genomes]
rs12597529	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12925954	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12926007	0.85[ASN][1000 genomes]
rs12935145	0.93[ASN][1000 genomes]
rs1520229	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1520230	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1520231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1520232	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs1520234	1.00[CHB][hapmap];0.80[JPT][hapmap];0.93[ASN][1000 genomes]
rs1520236	0.87[JPT][hapmap]
rs1520241	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1520243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1532418	0.86[JPT][hapmap]
rs16942779	0.84[ASN][1000 genomes]
rs16968098	0.84[ASN][1000 genomes]
rs16968101	0.84[ASN][1000 genomes]
rs16968102	0.84[ASN][1000 genomes]
rs16968480	0.81[JPT][hapmap]
rs1850966	0.95[ASN][1000 genomes]
rs185394	0.89[ASN][1000 genomes]
rs1874457	0.93[ASN][1000 genomes]
rs1874458	0.93[ASN][1000 genomes]
rs1874459	0.93[ASN][1000 genomes]
rs1879260	0.93[ASN][1000 genomes]
rs1896755	0.84[ASN][1000 genomes]
rs1896756	0.84[ASN][1000 genomes]
rs1908723	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1915117	0.86[JPT][hapmap]
rs2088285	0.80[JPT][hapmap]
rs2115393	0.81[ASN][1000 genomes]
rs2280396	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs257335	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs257336	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs257337	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs257341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs257487	0.95[ASN][1000 genomes]
rs257490	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs257497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs257498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs257499	0.87[ASN][1000 genomes]
rs28216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34699531	0.84[ASN][1000 genomes]
rs34893901	0.84[ASN][1000 genomes]
rs35139	0.91[ASN][1000 genomes]
rs35140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs35145	0.90[ASN][1000 genomes]
rs35146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs35148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs35149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35155	0.89[ASN][1000 genomes]
rs35156	0.89[ASN][1000 genomes]
rs35157	0.88[ASN][1000 genomes]
rs35158	0.88[ASN][1000 genomes]
rs35159	0.88[ASN][1000 genomes]
rs35160	0.88[ASN][1000 genomes]
rs35161	0.88[ASN][1000 genomes]
rs35162	0.88[ASN][1000 genomes]
rs35163	0.89[ASN][1000 genomes]
rs35164	0.89[ASN][1000 genomes]
rs35165	0.86[ASN][1000 genomes]
rs35166	0.89[ASN][1000 genomes]
rs35167	0.89[ASN][1000 genomes]
rs35169	0.89[ASN][1000 genomes]
rs35170	0.89[ASN][1000 genomes]
rs35171	0.89[ASN][1000 genomes]
rs35176	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs35177	0.94[ASN][1000 genomes]
rs35178	0.98[ASN][1000 genomes]
rs35179	0.98[ASN][1000 genomes]
rs35180	0.99[ASN][1000 genomes]
rs35188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35192	0.94[CHB][hapmap];0.99[ASN][1000 genomes]
rs35193	0.97[ASN][1000 genomes]
rs35195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35205	0.99[ASN][1000 genomes]
rs35206	0.99[ASN][1000 genomes]
rs35208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs35214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35215	0.99[ASN][1000 genomes]
rs35216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35218	0.99[ASN][1000 genomes]
rs35219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35224	0.97[ASN][1000 genomes]
rs35226	0.83[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs35229	0.81[YRI][hapmap]
rs35263777	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35557609	0.84[ASN][1000 genomes]
rs35891857	0.84[ASN][1000 genomes]
rs369499	0.89[ASN][1000 genomes]
rs382418	0.89[ASN][1000 genomes]
rs385317	0.84[ASN][1000 genomes]
rs388039	0.89[ASN][1000 genomes]
rs396950	0.89[ASN][1000 genomes]
rs400182	0.89[ASN][1000 genomes]
rs40113	0.89[ASN][1000 genomes]
rs40115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs40116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs40510	0.89[ASN][1000 genomes]
rs406925	0.89[ASN][1000 genomes]
rs408330	0.84[ASN][1000 genomes]
rs422274	0.89[ASN][1000 genomes]
rs42863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs436962	0.85[ASN][1000 genomes]
rs437402	0.89[ASN][1000 genomes]
rs437408	0.89[ASN][1000 genomes]
rs447096	0.89[ASN][1000 genomes]
rs453866	0.83[ASN][1000 genomes]
rs462735	0.92[ASN][1000 genomes]
rs4967858	0.84[ASN][1000 genomes]
rs4967859	0.84[ASN][1000 genomes]
rs4967860	0.84[ASN][1000 genomes]
rs4967861	0.84[ASN][1000 genomes]
rs4967862	0.84[ASN][1000 genomes]
rs4967866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4967875	0.84[ASN][1000 genomes]
rs4967876	0.84[ASN][1000 genomes]
rs4967882	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs4967886	0.80[JPT][hapmap]
rs59954387	0.91[ASN][1000 genomes]
rs610896	0.84[ASN][1000 genomes]
rs611241	0.84[ASN][1000 genomes]
rs611322	0.84[ASN][1000 genomes]
rs62042237	0.95[ASN][1000 genomes]
rs7188339	0.82[ASN][1000 genomes]
rs7189660	0.82[ASN][1000 genomes]
rs7204729	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7498801	0.80[JPT][hapmap]
rs8048351	0.84[EUR][1000 genomes]
rs8048383	0.85[ASN][1000 genomes]
rs878359	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs909003	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];0.97[ASN][1000 genomes]
rs973200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs974782	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs990639	0.95[ASN][1000 genomes]
rs9935608	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv948640	chr16:64859061-65112790	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:64991400-65032600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr16:64998000-65024800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr16:65000800-65051000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:65003400-65034000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr16:65004800-65027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:65006600-65020600	Weak transcription	Brain Germinal Matrix	brain
7	chr16:65006600-65021000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr16:65006600-65024800	Weak transcription	Spleen	Spleen
9	chr16:65007000-65020200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr16:65007000-65020800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr16:65008600-65024000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr16:65013400-65018000	Strong transcription	Fetal Lung	lung
13	chr16:65014200-65018000	Enhancers	Fetal Heart	heart
14	chr16:65014200-65040200	Weak transcription	Fetal Intestine Small	intestine
15	chr16:65014400-65020200	Weak transcription	NHLF	lung
16	chr16:65015000-65020600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr16:65015000-65035000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:65015800-65018600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr16:65016000-65018000	Enhancers	Brain Angular Gyrus	brain
20	chr16:65016000-65018600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr16:65016000-65020400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr16:65016000-65020800	Weak transcription	Fetal Intestine Large	intestine
23	chr16:65016200-65018000	Weak transcription	Placenta	Placenta
24	chr16:65016200-65019400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr16:65016200-65019400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr16:65016200-65020200	Weak transcription	Aorta	Aorta
27	chr16:65016200-65021600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:65016200-65025000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr16:65016200-65032400	Weak transcription	Lung	lung
30	chr16:65016200-65040200	Weak transcription	Left Ventricle	heart
31	chr16:65016600-65018200	Enhancers	Brain Hippocampus Middle	brain
32	chr16:65016600-65018200	Enhancers	Brain Substantia Nigra	brain
33	chr16:65016600-65018800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr16:65016600-65020400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr16:65016800-65019000	Weak transcription	NHDF-Ad	bronchial
36	chr16:65016800-65020400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr16:65016800-65021400	Weak transcription	HMEC	breast
38	chr16:65017000-65018000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr16:65017000-65021800	Weak transcription	Fetal Kidney	kidney
40	chr16:65017200-65018200	Enhancers	Brain Cingulate Gyrus	brain
41	chr16:65017200-65018400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr16:65017200-65018400	Enhancers	Brain Anterior Caudate	brain
43	chr16:65017200-65019000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr16:65017200-65041800	Weak transcription	Colon Smooth Muscle	Colon
45	chr16:65017400-65018000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr16:65017400-65018200	Enhancers	Fetal Brain Male	brain
47	chr16:65017400-65018400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:65017400-65018400	Genic enhancers	Fetal Stomach	stomach
49	chr16:65017400-65018800	Genic enhancers	Osteobl	bone
50	chr16:65017400-65020400	Weak transcription	Fetal Brain Female	brain

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