Variant report

Variant	rs12903900
Chromosome Location	chr15:92553489-92553490
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:92552941..92555827-chr15:92557594..92560539,2	MCF-7	breast:
2	chr15:92552040..92555185-chr15:92557169..92559357,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10468145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593984	0.87[CHB][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12904266	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12905905	0.83[JPT][hapmap]
rs12905912	0.92[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12906289	0.81[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs12908689	0.91[ASN][1000 genomes]
rs12912272	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12912997	1.00[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1983351	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs62011574	0.91[ASN][1000 genomes]
rs6496886	0.86[ASN][1000 genomes]
rs7178378	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7495052	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8040010	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048635	chr15:92073294-92557339	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904498	chr15:92545284-92558234	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12903900	VPS33B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92498200-92555000	Weak transcription	Gastric	stomach
2	chr15:92538200-92554800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr15:92544200-92554800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:92544400-92554800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:92544800-92554200	Weak transcription	Fetal Brain Female	brain
6	chr15:92544800-92554800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:92545400-92554800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:92547600-92555000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:92548200-92554200	Weak transcription	Primary T cells from cord blood	blood
10	chr15:92549000-92554800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:92549200-92554200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:92549200-92554600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:92549200-92555000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:92549400-92554800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:92549600-92554200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:92549600-92554200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:92549600-92555400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:92549800-92554200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:92549800-92555000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr15:92550200-92553600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:92550400-92556200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr15:92550600-92555000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:92550800-92562600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:92551000-92555000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:92551200-92556400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr15:92551200-92557400	Enhancers	Ovary	ovary
27	chr15:92551400-92555000	Enhancers	Brain Hippocampus Middle	brain
28	chr15:92551600-92555000	Weak transcription	Adipose Nuclei	Adipose
29	chr15:92551600-92556000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:92551800-92554200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:92551800-92554200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr15:92551800-92554200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:92552000-92554200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:92552200-92554800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:92552200-92555000	Enhancers	Brain Anterior Caudate	brain
36	chr15:92552200-92559000	Enhancers	Left Ventricle	heart
37	chr15:92552600-92554800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:92552800-92554000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr15:92552800-92554000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr15:92552800-92554200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:92552800-92554800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:92552800-92554800	Enhancers	Brain Cingulate Gyrus	brain
43	chr15:92552800-92554800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:92552800-92554800	Weak transcription	Lung	lung
45	chr15:92552800-92555000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:92552800-92561800	Weak transcription	Psoas Muscle	Psoas
47	chr15:92553000-92553600	Enhancers	Right Ventricle	heart
48	chr15:92553000-92554200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:92553000-92554800	Weak transcription	Fetal Heart	heart
50	chr15:92553000-92555200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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