Variant report

Variant	rs16860962
Chromosome Location	chr3:113154905-113154906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10511325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917149	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917288	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922598	0.83[JPT][hapmap]
rs11922838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924109	1.00[EUR][1000 genomes]
rs11926687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513288	0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs16845106	0.91[JPT][hapmap]
rs16845109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861109	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs16861217	0.87[EUR][1000 genomes]
rs17255950	0.91[EUR][1000 genomes]
rs17256551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17256752	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17322613	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17325024	0.87[EUR][1000 genomes]
rs1906141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989359	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs2129431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271496	0.87[EUR][1000 genomes]
rs2291412	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306068	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs2306070	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs28472841	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35758075	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35812463	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814399	0.92[JPT][hapmap]
rs56685963	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56772417	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57115529	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57164268	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57366942	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58905600	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58988763	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59271111	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59493419	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59673391	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59742486	0.84[EUR][1000 genomes]
rs60582065	0.84[EUR][1000 genomes]
rs60697865	0.91[EUR][1000 genomes]
rs60940543	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61065093	1.00[EUR][1000 genomes]
rs61575357	0.87[EUR][1000 genomes]
rs61594119	0.84[EUR][1000 genomes]
rs6438150	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438151	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783691	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs735	0.91[EUR][1000 genomes]
rs7610552	0.86[EUR][1000 genomes];1.00[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:113134600-113159800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:113135200-113164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:113136000-113176400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:113137400-113160000	Weak transcription	Fetal Stomach	stomach
7	chr3:113140000-113160000	Weak transcription	Psoas Muscle	Psoas
8	chr3:113145800-113155800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:113145800-113159400	Weak transcription	Gastric	stomach
10	chr3:113145800-113159400	Weak transcription	HSMMtube	muscle
11	chr3:113145800-113159600	Weak transcription	Lung	lung
12	chr3:113145800-113159800	Weak transcription	Esophagus	oesophagus
13	chr3:113145800-113159800	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:113145800-113159800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:113145800-113159800	Weak transcription	Thymus	Thymus
16	chr3:113145800-113160000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:113145800-113160200	Weak transcription	Aorta	Aorta
18	chr3:113145800-113166000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:113145800-113176600	Weak transcription	Spleen	Spleen
20	chr3:113146000-113155400	Weak transcription	Osteobl	bone
21	chr3:113146000-113155800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:113146000-113159800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:113146000-113160000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr3:113146000-113160000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:113146000-113160200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:113146000-113172000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:113146000-113191000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:113146200-113155400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:113146200-113159600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:113146200-113159600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:113146200-113159600	Weak transcription	Dnd41	blood
32	chr3:113146200-113160000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:113146200-113160000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:113146200-113160200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:113146200-113178600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:113146400-113159000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:113146400-113160000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:113146400-113165000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:113146800-113155400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:113147000-113159800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:113147000-113159800	Weak transcription	Adipose Nuclei	Adipose
42	chr3:113147000-113165600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:113147200-113155400	Weak transcription	Fetal Intestine Large	intestine
44	chr3:113147200-113159400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:113147200-113159600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:113147200-113160200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:113147400-113155400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:113147400-113159800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:113147400-113165400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:113147600-113159400	Weak transcription	A549	lung

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