Variant report

Variant	rs16977582
Chromosome Location	chr15:57829298-57829299
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	chr15:57827683..57829529-chr15:57832472..57835123,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11517	0.80[ASN][1000 genomes]
rs11545026	0.80[ASN][1000 genomes]
rs1280364	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1690319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1690320	0.80[ASN][1000 genomes]
rs16977594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16977597	0.80[ASN][1000 genomes]
rs1908193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2131732	0.80[ASN][1000 genomes]
rs2279608	0.80[ASN][1000 genomes]
rs2279609	0.80[ASN][1000 genomes]
rs2414514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2641567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs28379960	0.93[ASN][1000 genomes]
rs28507301	0.93[ASN][1000 genomes]
rs2922229	1.00[CHB][hapmap]
rs2934424	0.80[ASN][1000 genomes]
rs55924857	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57995724	0.93[ASN][1000 genomes]
rs6493932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7181371	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs74016263	0.85[ASN][1000 genomes]
rs74016266	0.85[ASN][1000 genomes]
rs74016268	1.00[ASN][1000 genomes]
rs74016270	1.00[ASN][1000 genomes]
rs74016271	1.00[ASN][1000 genomes]
rs9744909	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv833022	chr15:57657412-57830112	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16977582	CCPG1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57802600-57846600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:57803200-57842800	Weak transcription	Aorta	Aorta
3	chr15:57819200-57841000	Weak transcription	Esophagus	oesophagus
4	chr15:57819800-57833000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:57819800-57840000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:57820200-57829400	Weak transcription	Brain Angular Gyrus	brain
7	chr15:57820600-57834000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:57821800-57842800	Strong transcription	Liver	Liver
9	chr15:57822800-57833000	Weak transcription	HepG2	liver
10	chr15:57822800-57834000	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:57825000-57835800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:57825400-57831200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:57826000-57834200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:57827000-57829600	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr15:57827200-57830000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:57827200-57832200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:57827400-57832000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:57827400-57834200	Weak transcription	Lung	lung
19	chr15:57827600-57830200	Weak transcription	Fetal Stomach	stomach
20	chr15:57827600-57840600	Weak transcription	Fetal Lung	lung
21	chr15:57828000-57833400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:57828200-57830000	Weak transcription	Psoas Muscle	Psoas
23	chr15:57828200-57831800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:57828400-57830800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:57828600-57830600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:57828600-57830600	Enhancers	NHDF-Ad	bronchial
27	chr15:57828600-57832400	Enhancers	Fetal Kidney	kidney
28	chr15:57828800-57829400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr15:57828800-57829400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr15:57828800-57829400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:57828800-57829400	Enhancers	Left Ventricle	heart
32	chr15:57828800-57830000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:57828800-57830000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:57828800-57830000	Enhancers	Pancreas	Pancrea
35	chr15:57828800-57830200	Enhancers	Osteobl	bone
36	chr15:57829000-57829400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr15:57829000-57829400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
38	chr15:57829000-57829400	Enhancers	Brain Hippocampus Middle	brain
39	chr15:57829000-57829400	Enhancers	Right Atrium	heart
40	chr15:57829000-57829600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:57829000-57829600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:57829000-57829600	Enhancers	Gastric	stomach
43	chr15:57829000-57829600	Enhancers	Right Ventricle	heart
44	chr15:57829000-57829800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:57829000-57829800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr15:57829000-57829800	Flanking Active TSS	HSMMtube	muscle
47	chr15:57829000-57830000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:57829000-57830000	Enhancers	Stomach Mucosa	stomach
49	chr15:57829000-57830000	Enhancers	NHLF	lung
50	chr15:57829000-57830200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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