Variant report

Variant	rs12439793
Chromosome Location	chr15:57831197-57831198
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57829364..57831242-chr15:57841384..57843647,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11856674	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439291	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs12439292	0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs12439665	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1620402	0.81[CHD][hapmap]
rs1623697	0.81[CHD][hapmap]
rs1666573	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820431	1.00[ASW][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820437	0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820449	0.88[ASN][1000 genomes]
rs17820461	0.90[ASN][1000 genomes]
rs17820467	0.90[ASN][1000 genomes]
rs2131730	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs2131731	0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs2270488	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2279606	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2934418	0.90[ASN][1000 genomes]
rs3742963	0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs3742964	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4774961	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4774962	0.92[ASN][1000 genomes]
rs55777040	1.00[AFR][1000 genomes]
rs55916627	0.92[ASN][1000 genomes]
rs55952634	0.92[ASN][1000 genomes]
rs56362917	0.92[ASN][1000 genomes]
rs59368768	0.92[ASN][1000 genomes]
rs66802357	0.82[ASN][1000 genomes]
rs67336499	0.92[ASN][1000 genomes]
rs7166305	0.92[ASN][1000 genomes]
rs7171354	0.81[ASN][1000 genomes]
rs7171360	0.92[ASN][1000 genomes]
rs72741522	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72741528	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8025786	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937248	0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12439793	TMOD3	cis	parietal	SCAN
rs12439793	CCNB2	cis	parietal	SCAN

Chromatin state (count:54 , 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	chr15:57820600-57834000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:57821800-57842800	Strong transcription	Liver	Liver
8	chr15:57822800-57833000	Weak transcription	HepG2	liver
9	chr15:57822800-57834000	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:57825000-57835800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:57825400-57831200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:57826000-57834200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:57827200-57832200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:57827400-57832000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:57827400-57834200	Weak transcription	Lung	lung
16	chr15:57827600-57840600	Weak transcription	Fetal Lung	lung
17	chr15:57828000-57833400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:57828200-57831800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr15:57828600-57832400	Enhancers	Fetal Kidney	kidney
20	chr15:57829000-57832000	Enhancers	Fetal Muscle Leg	muscle
21	chr15:57829400-57832600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:57829400-57835800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:57829400-57841200	Weak transcription	Left Ventricle	heart
24	chr15:57829400-57842600	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:57829600-57831400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr15:57829600-57831400	Weak transcription	Gastric	stomach
27	chr15:57829600-57832200	Enhancers	Fetal Muscle Trunk	muscle
28	chr15:57829600-57834600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:57829600-57834600	Weak transcription	Right Ventricle	heart
30	chr15:57829600-57835800	Weak transcription	Ovary	ovary
31	chr15:57829600-57842000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:57829600-57843200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:57829800-57833200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:57830000-57831400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr15:57830000-57832400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:57830000-57833000	Weak transcription	Placenta	Placenta
37	chr15:57830000-57833000	Weak transcription	Pancreas	Pancrea
38	chr15:57830000-57834200	Weak transcription	Stomach Mucosa	stomach
39	chr15:57830000-57840800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:57830000-57846400	Weak transcription	Brain Substantia Nigra	brain
41	chr15:57830200-57842200	Strong transcription	Fetal Stomach	stomach
42	chr15:57830400-57831800	Weak transcription	HSMMtube	muscle
43	chr15:57830400-57843400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:57830600-57834400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:57830600-57835400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:57830600-57842200	Weak transcription	Brain Anterior Caudate	brain
47	chr15:57830800-57831200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
48	chr15:57830800-57831600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:57830800-57831800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:57830800-57831800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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