Variant report

Variant	rs3131827
Chromosome Location	chr1:92711067-92711068
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10159094	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10875209	1.00[JPT][hapmap]
rs10875214	1.00[JPT][hapmap]
rs10875319	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875349	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11164288	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11164349	0.91[EUR][1000 genomes]
rs11164546	0.80[ASN][1000 genomes]
rs11166042	1.00[JPT][hapmap]
rs11166141	1.00[JPT][hapmap]
rs11166144	1.00[JPT][hapmap]
rs1157470	1.00[JPT][hapmap]
rs11577572	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11580693	0.90[ASN][1000 genomes]
rs11585255	1.00[JPT][hapmap]
rs11588044	1.00[JPT][hapmap]
rs11588153	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11589858	1.00[JPT][hapmap]
rs11803383	0.81[EUR][1000 genomes]
rs11803457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12024731	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12086394	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119246	1.00[JPT][hapmap]
rs1226183	1.00[JPT][hapmap]
rs1226187	1.00[JPT][hapmap]
rs12404806	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12406749	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12407622	1.00[JPT][hapmap]
rs12411162	0.90[ASN][1000 genomes]
rs12729867	1.00[JPT][hapmap]
rs12740246	1.00[JPT][hapmap]
rs12749317	0.90[ASN][1000 genomes]
rs12755781	1.00[JPT][hapmap]
rs12757533	1.00[JPT][hapmap]
rs1483022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1487536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1487540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17519972	1.00[JPT][hapmap]
rs1872007	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1982720	1.00[JPT][hapmap]
rs2046620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093879	1.00[JPT][hapmap]
rs2128645	1.00[JPT][hapmap]
rs2128646	1.00[JPT][hapmap]
rs2391114	1.00[JPT][hapmap]
rs2391158	1.00[JPT][hapmap]
rs2391161	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2839877	1.00[JPT][hapmap]
rs2893200	1.00[JPT][hapmap]
rs3103170	0.87[EUR][1000 genomes]
rs3103176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3103181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122321	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122323	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3122325	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3122327	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131813	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131820	0.96[CEU][hapmap]
rs3131828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851271	1.00[JPT][hapmap]
rs3851272	1.00[JPT][hapmap]
rs3851273	1.00[JPT][hapmap]
rs3929737	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4393167	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4414050	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4437922	1.00[JPT][hapmap]
rs4658128	1.00[JPT][hapmap]
rs4658290	1.00[JPT][hapmap]
rs4658294	1.00[JPT][hapmap]
rs4658297	0.90[ASN][1000 genomes]
rs4658298	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4658299	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4658300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs488849	1.00[JPT][hapmap]
rs490800	1.00[JPT][hapmap]
rs492164	1.00[JPT][hapmap]
rs493595	1.00[JPT][hapmap]
rs4949888	1.00[JPT][hapmap]
rs504606	1.00[JPT][hapmap]
rs506375	1.00[JPT][hapmap]
rs507452	1.00[JPT][hapmap]
rs511546	1.00[JPT][hapmap]
rs515280	1.00[JPT][hapmap]
rs519932	1.00[JPT][hapmap]
rs527412	1.00[JPT][hapmap]
rs529135	1.00[JPT][hapmap]
rs534547	1.00[JPT][hapmap]
rs547699	1.00[JPT][hapmap]
rs553861	1.00[JPT][hapmap]
rs556980	1.00[JPT][hapmap]
rs563113	1.00[JPT][hapmap]
rs563606	1.00[JPT][hapmap]
rs569593	1.00[JPT][hapmap]
rs570368	1.00[JPT][hapmap]
rs573044	1.00[JPT][hapmap]
rs575805	1.00[JPT][hapmap]
rs6603962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6603971	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6604080	1.00[JPT][hapmap]
rs6604082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6604088	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6604090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6661384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6663114	0.89[EUR][1000 genomes]
rs6663118	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6663278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668803	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66758257	0.90[ASN][1000 genomes]
rs6684317	1.00[JPT][hapmap]
rs6689366	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6692287	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6699855	1.00[JPT][hapmap]
rs6702267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs733012	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs745793	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7517541	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518974	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7520275	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7533077	1.00[JPT][hapmap]
rs7539757	0.80[ASN][1000 genomes]
rs7542358	1.00[JPT][hapmap]
rs7542373	1.00[JPT][hapmap]
rs7543947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545076	1.00[JPT][hapmap]
rs912794	0.90[EUR][1000 genomes]
rs9440085	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs981583	1.00[JPT][hapmap]
rs9943178	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92705600-92726800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:92705800-92711400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:92705800-92729200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:92707200-92764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:92708200-92741200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:92708600-92711400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:92708600-92712000	Weak transcription	Osteobl	bone
8	chr1:92708800-92712200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:92709000-92711200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:92709000-92711600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:92709000-92711600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:92709000-92711600	Weak transcription	HUVEC	blood vessel
13	chr1:92709000-92712000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:92709000-92712200	Weak transcription	Fetal Lung	lung
15	chr1:92709000-92712200	Weak transcription	Fetal Stomach	stomach
16	chr1:92709000-92717400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:92709000-92718800	Weak transcription	Lung	lung
18	chr1:92709000-92737200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:92709000-92762800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:92709200-92712200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:92709200-92718800	Weak transcription	Pancreas	Pancrea
22	chr1:92709400-92711200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:92709400-92711400	Weak transcription	Fetal Intestine Large	intestine
24	chr1:92709400-92712200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:92709400-92712200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:92709400-92712400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:92709400-92735800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:92709600-92711400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:92709600-92730800	Weak transcription	Hela-S3	cervix
30	chr1:92709800-92711400	Weak transcription	Fetal Thymus	thymus
31	chr1:92710000-92711600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr1:92710000-92711600	Weak transcription	Primary T cells from cord blood	blood
33	chr1:92710000-92711600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:92710000-92711600	Weak transcription	Liver	Liver
35	chr1:92710000-92712200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:92710000-92712200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:92710000-92712200	Weak transcription	Primary B cells from cord blood	blood
38	chr1:92710000-92712200	Weak transcription	Brain Anterior Caudate	brain
39	chr1:92710000-92712200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:92710000-92712200	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:92710000-92712200	Weak transcription	Ovary	ovary
42	chr1:92710000-92712200	Weak transcription	Thymus	Thymus
43	chr1:92710000-92717800	Weak transcription	Brain Germinal Matrix	brain
44	chr1:92710000-92737600	Weak transcription	HSMM	muscle
45	chr1:92710000-92745200	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:92710200-92715000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:92710200-92717400	Weak transcription	Adipose Nuclei	Adipose
48	chr1:92710200-92717800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:92710200-92717800	Weak transcription	Placenta	Placenta
50	chr1:92710200-92718000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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