Variant report

Variant	rs2899492
Chromosome Location	chr15:52933262-52933263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52931519..52933404-chr15:52936579..52938944,2	MCF-7	breast:
2	chr15:52927735..52930583-chr15:52932709..52935463,2	K562	blood:
3	chr15:52932870..52937961-chr15:52968619..52973908,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1080731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851520	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10851521	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11070907	1.00[CHB][hapmap]
rs11070909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11853917	1.00[CHB][hapmap]
rs11855616	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11857150	1.00[CHB][hapmap]
rs12594964	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12898644	1.00[CHB][hapmap]
rs12902679	1.00[CHB][hapmap]
rs12914502	1.00[CHB][hapmap]
rs12915981	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs13329393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17614559	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs17651941	0.82[EUR][1000 genomes]
rs1863512	0.89[CHB][hapmap]
rs2288271	1.00[CHB][hapmap]
rs2414160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2414161	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2414163	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2414166	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2414167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28368342	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3751614	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs4390542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4548810	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4636853	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774634	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4776058	1.00[CHB][hapmap]
rs4776063	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4776065	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs4776066	1.00[CHB][hapmap]
rs55895733	0.81[EUR][1000 genomes]
rs7167494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026800	1.00[CHB][hapmap]
rs8030141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8036979	0.80[EUR][1000 genomes]
rs933860	1.00[CHB][hapmap];0.82[CHD][hapmap]

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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
2	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
3	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:52872200-52933800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
7	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:52902200-52943800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:52902400-52934800	Weak transcription	NH-A	brain
12	chr15:52902600-52942000	Weak transcription	HUVEC	blood vessel
13	chr15:52903400-52933800	Weak transcription	Fetal Heart	heart
14	chr15:52903400-52943800	Weak transcription	Hela-S3	cervix
15	chr15:52903400-52944000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:52903600-52942400	Weak transcription	Dnd41	blood
17	chr15:52903600-52945400	Weak transcription	Colonic Mucosa	Colon
18	chr15:52904000-52934400	Weak transcription	Fetal Brain Male	brain
19	chr15:52904000-52943400	Weak transcription	Fetal Kidney	kidney
20	chr15:52904000-52945400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
22	chr15:52906200-52934200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:52906200-52944000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:52908600-52956200	Weak transcription	Gastric	stomach
25	chr15:52909000-52942400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:52909600-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
28	chr15:52915600-52944200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:52915800-52938400	Weak transcription	Ovary	ovary
30	chr15:52916200-52934800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr15:52916200-52942800	Weak transcription	Fetal Brain Female	brain
32	chr15:52916800-52934400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:52916800-52934800	Weak transcription	Brain Substantia Nigra	brain
34	chr15:52916800-52936000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:52917000-52938400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:52917000-52943600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:52920800-52942800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:52921000-52934400	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:52921800-52939400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr15:52921800-52939600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:52922200-52934400	Strong transcription	Primary B cells from cord blood	blood
42	chr15:52922400-52933400	Weak transcription	GM12878-XiMat	blood
43	chr15:52922800-52933400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:52923200-52945200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr15:52924200-52934400	Weak transcription	Brain Anterior Caudate	brain
46	chr15:52925800-52934400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:52925800-52934400	Weak transcription	Colon Smooth Muscle	Colon
48	chr15:52925800-52935000	Weak transcription	Psoas Muscle	Psoas
49	chr15:52925800-52935400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:52926000-52933600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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