Variant report

Variant	rs8039450
Chromosome Location	chr15:30068673-30068674
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:30066918..30068960-chr15:30070446..30071982,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11853814	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12899253	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12902476	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12916720	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs260530	0.86[ASN][1000 genomes]
rs260537	0.84[ASN][1000 genomes]
rs3784353	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4553573	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7495511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8039450	SNORD115-38	cis	cerebellum	SCAN
rs8039450	MAGEL2	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30021400-30097200	Weak transcription	Aorta	Aorta
2	chr15:30050200-30070600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:30052000-30070600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:30052600-30089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:30053000-30072600	Weak transcription	Spleen	Spleen
6	chr15:30058600-30092200	Weak transcription	Esophagus	oesophagus
7	chr15:30058600-30106000	Weak transcription	Gastric	stomach
8	chr15:30059800-30086200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:30060600-30071200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:30060800-30069200	Weak transcription	Right Atrium	heart
11	chr15:30060800-30076800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:30062400-30072600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:30062800-30096600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:30063000-30072600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:30063600-30069000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:30063600-30072600	Weak transcription	Lung	lung
17	chr15:30063600-30073400	Weak transcription	Fetal Lung	lung
18	chr15:30063800-30068800	Weak transcription	Liver	Liver
19	chr15:30063800-30069000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:30063800-30070400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:30063800-30070800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:30063800-30071000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:30063800-30076800	Weak transcription	Fetal Kidney	kidney
24	chr15:30063800-30096000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:30063800-30096800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:30064000-30069200	Weak transcription	Ovary	ovary
27	chr15:30064000-30072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:30064000-30085600	Weak transcription	Fetal Stomach	stomach
29	chr15:30064000-30085800	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:30064200-30069000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:30064200-30070800	Weak transcription	Adipose Nuclei	Adipose
32	chr15:30064200-30071600	Enhancers	Brain Substantia Nigra	brain
33	chr15:30064200-30073600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:30064400-30083800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:30065200-30103400	Weak transcription	Placenta	Placenta
36	chr15:30065600-30068800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:30065600-30072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:30065600-30085400	Weak transcription	Fetal Intestine Large	intestine
39	chr15:30065600-30090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:30065600-30094400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:30065600-30094400	Weak transcription	Fetal Intestine Small	intestine
42	chr15:30065600-30108200	Weak transcription	Pancreas	Pancrea
43	chr15:30065800-30069800	Enhancers	Brain Hippocampus Middle	brain
44	chr15:30066000-30068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:30066000-30072200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:30066400-30069400	Enhancers	Brain Angular Gyrus	brain
47	chr15:30066400-30071800	Enhancers	Brain Cingulate Gyrus	brain
48	chr15:30066600-30068800	Weak transcription	Fetal Heart	heart
49	chr15:30067200-30069600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:30067400-30069000	Enhancers	Colon Smooth Muscle	Colon

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