Variant report

Variant	rs2899469
Chromosome Location	chr15:51481922-51481923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51471485..51476477-chr15:51478352..51482224,6	MCF-7	breast:
2	chr15:51477370..51478927-chr15:51479650..51482027,2	K562	blood:
3	chr15:51479346..51482032-chr15:51482549..51485110,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10046	0.81[CEU][hapmap]
rs1065779	0.81[CEU][hapmap]
rs12148604	0.80[CEU][hapmap]
rs12441919	0.82[ASN][1000 genomes]
rs12591172	0.81[CEU][hapmap]
rs12592344	0.85[ASN][1000 genomes]
rs12594395	0.86[ASN][1000 genomes]
rs12708426	0.86[EUR][1000 genomes]
rs12904291	0.85[ASN][1000 genomes]
rs13353155	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1438921	0.81[ASN][1000 genomes]
rs2289105	0.81[CEU][hapmap]
rs2304463	0.81[CEU][hapmap]
rs2414094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28591334	0.85[ASN][1000 genomes]
rs35373992	0.85[ASN][1000 genomes]
rs3784307	0.81[CEU][hapmap]
rs4551976	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774583	0.81[CEU][hapmap]
rs55658651	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55712458	0.85[ASN][1000 genomes]
rs8029120	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2899469	TMOD2	cis	cerebellum	SCAN
rs2899469	TNFAIP8L3	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51476400-51483000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:51476600-51485600	Weak transcription	Right Atrium	heart
3	chr15:51477000-51482200	Weak transcription	HepG2	liver
4	chr15:51477400-51482200	Weak transcription	Lung	lung
5	chr15:51478400-51483200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:51478600-51483400	Weak transcription	Fetal Intestine Small	intestine
7	chr15:51479000-51482200	Weak transcription	Brain Angular Gyrus	brain
8	chr15:51479000-51483400	Weak transcription	Stomach Mucosa	stomach
9	chr15:51479000-51484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:51479000-51485000	Enhancers	Right Ventricle	heart
11	chr15:51479200-51482000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:51479200-51482400	Weak transcription	Fetal Brain Male	brain
13	chr15:51479200-51482600	Weak transcription	Placenta	Placenta
14	chr15:51479200-51484600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:51479600-51483400	Weak transcription	HSMM	muscle
16	chr15:51479800-51483200	Weak transcription	HSMMtube	muscle
17	chr15:51480200-51482200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:51480400-51483400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:51480600-51483600	Weak transcription	Fetal Thymus	thymus
20	chr15:51480600-51485000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:51480800-51482600	Weak transcription	Esophagus	oesophagus
22	chr15:51481000-51482000	Weak transcription	Fetal Heart	heart
23	chr15:51481000-51483600	Enhancers	Brain Hippocampus Middle	brain
24	chr15:51481200-51482000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:51481200-51482200	Weak transcription	Left Ventricle	heart
26	chr15:51481200-51484600	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:51481600-51483600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr15:51481800-51482000	Enhancers	Aorta	Aorta
29	chr15:51481800-51482200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr15:51481800-51482400	Enhancers	Adipose Nuclei	Adipose
31	chr15:51481800-51482800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr15:51481800-51483600	Enhancers	Primary B cells from cord blood	blood
33	chr15:51481800-51483600	Enhancers	Brain Substantia Nigra	brain
34	chr15:51481800-51483800	Enhancers	Spleen	Spleen
35	chr15:51481800-51484800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:51481800-51485000	Enhancers	Fetal Muscle Leg	muscle

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