Variant report

Variant	rs754516
Chromosome Location	chr15:79288981-79288982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79287783..79290330-chr15:79294942..79296932,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11072823	0.89[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11852934	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12900315	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12902783	0.81[EUR][1000 genomes]
rs12903619	0.81[CEU][hapmap]
rs12914556	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1867315	0.89[ASW][hapmap]
rs3784528	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs3784530	0.86[EUR][1000 genomes]
rs3784531	0.87[EUR][1000 genomes]
rs3784533	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs3816284	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4778753	0.81[CEU][hapmap]
rs6495358	0.83[EUR][1000 genomes]
rs894782	0.93[ASN][1000 genomes]
rs894783	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904433	chr15:79243571-79310288	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs754516	IMP3	cis	cerebellum	SCAN
rs754516	SH2D7	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79276400-79309200	Weak transcription	Right Atrium	heart
2	chr15:79278400-79290400	Enhancers	Fetal Intestine Small	intestine
3	chr15:79279600-79291000	Enhancers	Fetal Intestine Large	intestine
4	chr15:79281600-79290200	Weak transcription	Brain Substantia Nigra	brain
5	chr15:79281800-79296000	Weak transcription	Primary B cells from cord blood	blood
6	chr15:79281800-79296600	Weak transcription	Esophagus	oesophagus
7	chr15:79281800-79296600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:79282400-79289200	Weak transcription	HMEC	breast
9	chr15:79282600-79289000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:79282600-79289200	Weak transcription	NH-A	brain
11	chr15:79283000-79295000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:79284600-79289200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:79285200-79290800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:79285600-79289000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:79285600-79290400	Weak transcription	Brain Anterior Caudate	brain
16	chr15:79285600-79294400	Weak transcription	HSMM	muscle
17	chr15:79285800-79290200	Weak transcription	GM12878-XiMat	blood
18	chr15:79285800-79294600	Weak transcription	Brain Angular Gyrus	brain
19	chr15:79285800-79298400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:79286400-79290800	Weak transcription	Placenta	Placenta
21	chr15:79286800-79289200	Weak transcription	HSMMtube	muscle
22	chr15:79286800-79290200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:79286800-79290400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr15:79287000-79289200	Enhancers	HepG2	liver
25	chr15:79287000-79290400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr15:79287000-79290400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:79287200-79325800	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:79287800-79289400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr15:79288000-79289400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr15:79288000-79291200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:79288000-79293600	Strong transcription	Pancreatic Islets	Pancreatic Islet
32	chr15:79288200-79289000	Enhancers	Spleen	Spleen
33	chr15:79288200-79289400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr15:79288200-79289600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr15:79288200-79290800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr15:79288400-79289200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr15:79288400-79289400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr15:79288400-79289400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:79288400-79289400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:79288400-79289600	Enhancers	A549	lung
41	chr15:79288400-79290000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:79288400-79295400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:79288600-79289000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:79288600-79289000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:79288600-79289200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr15:79288600-79289200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr15:79288600-79289400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:79288600-79289600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:79288600-79289800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:79288800-79289400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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