Variant report

Variant	rs28729666
Chromosome Location	chr15:99903964-99903965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12148825	0.85[EUR][1000 genomes]
rs1510059	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289558	0.87[ASN][1000 genomes]
rs28651946	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4471659	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4545797	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4640164	0.80[EUR][1000 genomes]
rs58762669	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59136665	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59855164	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62023803	0.82[EUR][1000 genomes]
rs62023806	0.87[EUR][1000 genomes]
rs62023807	0.80[EUR][1000 genomes]
rs62023809	0.89[EUR][1000 genomes]
rs62023810	0.85[EUR][1000 genomes]
rs62023811	0.89[EUR][1000 genomes]
rs62023846	0.83[EUR][1000 genomes]
rs62023847	0.83[EUR][1000 genomes]
rs62023852	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62023854	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62023857	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62023858	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025360	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62025361	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62025363	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62025364	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62025365	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62025366	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62025367	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62025382	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62025383	0.90[ASN][1000 genomes]
rs6422002	0.85[EUR][1000 genomes]
rs7167033	0.89[EUR][1000 genomes]
rs7181876	0.82[EUR][1000 genomes]
rs7181973	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs768159	0.90[ASN][1000 genomes]
rs8032790	0.85[EUR][1000 genomes]
rs8033188	0.87[EUR][1000 genomes]
rs8041236	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978703	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	96 gene(s)	inside rSNPs	diseases
2	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats 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 target site	41 gene(s)	inside rSNPs	diseases
11	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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 target site	19 gene(s)	inside rSNPs	diseases
14	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
15	nsv1052683	chr15:99869631-99924685	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv542521	chr15:99869631-99924685	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99859400-99906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:99867200-99926600	Weak transcription	NHEK	skin
3	chr15:99872000-99906600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:99872000-99912600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:99872600-99909000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:99872800-99906200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:99872800-99911400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:99874600-99906600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr15:99877800-99906200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:99878200-99906600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr15:99880000-99906200	Weak transcription	Small Intestine	intestine
12	chr15:99881400-99906200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:99882000-99905000	Weak transcription	Brain Anterior Caudate	brain
14	chr15:99882200-99908600	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:99882600-99906200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:99882600-99908800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:99882600-99911200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:99882600-99925200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:99882800-99906200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:99882800-99908600	Weak transcription	Placenta	Placenta
21	chr15:99884400-99905200	Weak transcription	Gastric	stomach
22	chr15:99884400-99910400	Weak transcription	Brain Substantia Nigra	brain
23	chr15:99884600-99910800	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:99885200-99906000	Weak transcription	NHDF-Ad	bronchial
25	chr15:99885400-99911800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:99885400-99916000	Weak transcription	Fetal Heart	heart
27	chr15:99886600-99906400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:99886600-99911400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:99886600-99931400	Weak transcription	Esophagus	oesophagus
30	chr15:99890800-99908600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:99891400-99904600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr15:99892000-99908400	Weak transcription	Fetal Brain Female	brain
33	chr15:99893600-99925400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:99893800-99906600	Weak transcription	Adipose Nuclei	Adipose
35	chr15:99893800-99911600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:99894000-99904200	Weak transcription	Pancreas	Pancrea
37	chr15:99894000-99905400	Weak transcription	Primary T cells from cord blood	blood
38	chr15:99894000-99906400	Weak transcription	Aorta	Aorta
39	chr15:99894000-99907000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:99894000-99908600	Weak transcription	Psoas Muscle	Psoas
41	chr15:99894000-99925200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:99894200-99906200	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:99894200-99908600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:99895800-99905400	Weak transcription	Brain Angular Gyrus	brain
45	chr15:99896800-99904200	Weak transcription	A549	lung
46	chr15:99896800-99904800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:99899200-99908600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:99899800-99906400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:99900200-99909600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:99900400-99904400	Weak transcription	GM12878-XiMat	blood

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