Variant report

Variant	rs12439292
Chromosome Location	chr15:57842541-57842542
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57829364..57831242-chr15:57841384..57843647,2	MCF-7	breast:
2	chr15:57837700..57840998-chr15:57842272..57845131,4	MCF-7	breast:
3	chr15:57841937..57843856-chr15:57845649..57847200,2	K562	blood:
4	chr15:57842103..57844129-chr15:57847997..57849787,2	K562	blood:
5	chr15:57842103..57844046-chr15:57847997..57849926,2	K562	blood:

Variant related genes	Relation type
ENSG00000240874	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11856	0.94[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11856674	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs12439291	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439665	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12439793	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]
rs1626448	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1630903	0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1666572	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs1666573	0.95[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1690316	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1690317	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1690318	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17820431	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17820437	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17820449	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17820461	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17820467	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1908191	0.92[EUR][1000 genomes]
rs1908192	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2131730	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2131731	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2131733	0.89[EUR][1000 genomes]
rs2270487	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2270488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2279606	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[ASN][1000 genomes]
rs2635389	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2922231	0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2922232	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2932208	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2932209	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2934418	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3742963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742964	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774961	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774962	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55916627	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55952634	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56362917	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59368768	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66802357	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67336499	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166305	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171354	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171360	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72741522	0.94[ASN][1000 genomes]
rs72741528	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8025786	0.92[ASN][1000 genomes]
rs8038795	0.95[CEU][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs937248	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	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
4	nsv976938	chr15:57838920-57842883	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12439292	RNF111	cis	cerebellum	SCAN
rs12439292	CCNB2	cis	parietal	SCAN

Chromatin state (count:72 , 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	chr15:57821800-57842800	Strong transcription	Liver	Liver
4	chr15:57829400-57842600	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:57829600-57843200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:57830000-57846400	Weak transcription	Brain Substantia Nigra	brain
7	chr15:57830400-57843400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:57831400-57843400	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr15:57832400-57842600	Weak transcription	Fetal Kidney	kidney
10	chr15:57832400-57843200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:57834000-57843000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:57834800-57843600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:57835400-57843000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:57835800-57843200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:57836200-57843400	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr15:57837800-57853000	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:57839800-57842800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:57839800-57843400	Genic enhancers	Pancreas	Pancrea
19	chr15:57839800-57847800	Enhancers	Fetal Intestine Large	intestine
20	chr15:57840000-57843000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:57840000-57843000	Weak transcription	Placenta	Placenta
22	chr15:57840000-57843200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:57840000-57843200	Weak transcription	Lung	lung
24	chr15:57840000-57843400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:57840000-57843600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr15:57840000-57846600	Weak transcription	Ovary	ovary
27	chr15:57840200-57843000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:57840200-57843400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:57840400-57844600	Enhancers	Stomach Mucosa	stomach
30	chr15:57840600-57843600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr15:57840600-57847400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr15:57840800-57848000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:57840800-57849400	Enhancers	Fetal Muscle Leg	muscle
34	chr15:57841000-57843400	Weak transcription	HepG2	liver
35	chr15:57841000-57847800	Enhancers	Right Atrium	heart
36	chr15:57841000-57848000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr15:57841000-57848600	Enhancers	HSMMtube	muscle
38	chr15:57841200-57842800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:57841200-57843600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr15:57841200-57847600	Enhancers	Left Ventricle	heart
41	chr15:57841400-57842600	Enhancers	Gastric	stomach
42	chr15:57841400-57842800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:57841400-57843200	Weak transcription	Esophagus	oesophagus
44	chr15:57841400-57843400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr15:57841400-57843400	Weak transcription	Spleen	Spleen
46	chr15:57841400-57843800	Enhancers	Psoas Muscle	Psoas
47	chr15:57841600-57842800	Weak transcription	A549	lung
48	chr15:57841600-57843200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:57841600-57843200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:57841800-57842800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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