Variant report

Variant	rs2899493
Chromosome Location	chr15:52951166-52951167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52950435..52952896-chr15:52954166..52957098,2	K562	blood:
2	chr15:52938830..52941710-chr15:52949842..52951854,2	MCF-7	breast:
3	chr15:52951164..52953709-chr15:52956202..52958313,2	K562	blood:
4	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:
5	chr15:52950435..52952997-chr15:52969814..52971344,2	K562	blood:
6	chr15:52860334..52861897-chr15:52949806..52952761,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10775148	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10775149	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11070910	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11629479	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11634879	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12102061	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12900462	0.98[EUR][1000 genomes]
rs12908944	0.83[EUR][1000 genomes]
rs12916276	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12916405	0.95[EUR][1000 genomes]
rs2414162	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2414165	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2414168	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2414169	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2414170	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2414171	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2414174	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2414176	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2414177	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34340005	0.84[EUR][1000 genomes]
rs35756938	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35760898	0.89[EUR][1000 genomes]
rs4386077	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4404000	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4774635	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4776064	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62025584	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62025586	0.98[EUR][1000 genomes]
rs6493570	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7162184	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7166478	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7168045	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7169849	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026304	0.83[AMR][1000 genomes]
rs8026469	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8032889	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8035115	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8036671	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8036680	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8040787	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8042646	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs933858	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs933859	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9806267	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	37 gene(s)	inside rSNPs	diseases
4	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
3	chr15:52908600-52956200	Weak transcription	Gastric	stomach
4	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
6	chr15:52928000-52956400	Weak transcription	Lung	lung
7	chr15:52944200-52951800	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr15:52944200-52965800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:52944400-52957000	Weak transcription	Brain Germinal Matrix	brain
10	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:52944600-52962000	Weak transcription	Aorta	Aorta
13	chr15:52944600-52965000	Strong transcription	Primary B cells from cord blood	blood
14	chr15:52944600-52965400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:52944600-52969800	Weak transcription	Fetal Brain Male	brain
16	chr15:52944800-52952000	Strong transcription	Primary hematopoietic stem cells	blood
17	chr15:52945000-52965400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:52945000-52968600	Weak transcription	HepG2	liver
19	chr15:52945200-52959800	Weak transcription	Dnd41	blood
20	chr15:52945400-52951200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:52945400-52951600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr15:52945400-52956600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:52945400-52965400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr15:52945600-52956200	Weak transcription	Colonic Mucosa	Colon
25	chr15:52945600-52958400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:52945600-52962800	Strong transcription	Placenta	Placenta
27	chr15:52945800-52951400	Strong transcription	Primary T cells from cord blood	blood
28	chr15:52945800-52951400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:52945800-52956800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:52946000-52956800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:52946000-52956800	Weak transcription	Small Intestine	intestine
32	chr15:52946000-52962000	Weak transcription	Right Ventricle	heart
33	chr15:52946000-52962000	Weak transcription	Spleen	Spleen
34	chr15:52946000-52965200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr15:52946000-52968200	Weak transcription	Fetal Heart	heart
36	chr15:52946000-52968600	Weak transcription	Stomach Mucosa	stomach
37	chr15:52946400-52953400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:52946800-52959400	Weak transcription	Hela-S3	cervix
39	chr15:52947200-52952000	Enhancers	Brain Substantia Nigra	brain
40	chr15:52947400-52951600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:52947800-52951600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr15:52948000-52951400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr15:52948200-52954400	Weak transcription	Fetal Kidney	kidney
44	chr15:52948800-52951200	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr15:52949000-52951600	Enhancers	Brain Anterior Caudate	brain
46	chr15:52949200-52951400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:52949200-52965400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr15:52949200-52965600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:52949400-52951200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:52949400-52966400	Strong transcription	Duodenum Mucosa	Duodenum

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