Variant report

Variant	rs12439239
Chromosome Location	chr15:31651718-31651719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31643860..31648950-chr15:31650672..31654273,5	MCF-7	breast:
2	chr15:31647650..31653294-chr15:31653476..31658122,6	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1075232	0.89[AMR][1000 genomes]
rs12437749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437800	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438318	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12438813	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439853	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16956707	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16956738	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34959140	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4450360	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56396205	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58156651	0.82[AMR][1000 genomes]
rs66501706	0.88[ASN][1000 genomes]
rs66581165	0.84[AMR][1000 genomes]
rs67634762	0.84[AMR][1000 genomes]
rs72722829	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722847	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72722861	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72724938	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9672214	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9672538	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv1050482	chr15:31601016-31672921	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv1048082	chr15:31610245-31667000	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv1045944	chr15:31610245-31672921	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv516681	chr15:31616674-31675453	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv903841	chr15:31616674-31697242	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv903842	chr15:31621321-31697242	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv456748	chr15:31621321-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	nsv568801	chr15:31621321-31697642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv1052942	chr15:31624164-31653633	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1810782	chr15:31633161-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
19	nsv1051910	chr15:31641254-31672921	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12439239	RP11-932O9.7	cis	Artery Tibial	GTEx
rs12439239	CHRNA7	cis	Thyroid	GTEx
rs12439239	CTD-3092A11.2	cis	Whole Blood	GTEx
rs12439239	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs12439239	CHRNA7	cis	Whole Blood	GTEx
rs12439239	RP11-932O9.7	cis	lung	GTEx
rs12439239	CHRNA7	cis	Artery Tibial	GTEx
rs12439239	CHRNA7	cis	lung	GTEx
rs12439239	GOLGA8R	cis	Heart Left Ventricle	GTEx
rs12439239	CTD-3092A11.2	cis	lung	GTEx
rs12439239	CTD-3092A11.2	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31622800-31657400	Enhancers	Right Atrium	heart
2	chr15:31638400-31655400	Enhancers	Psoas Muscle	Psoas
3	chr15:31641000-31655600	Enhancers	Left Ventricle	heart
4	chr15:31641200-31658400	Enhancers	Liver	Liver
5	chr15:31645200-31652400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:31645200-31653200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:31645400-31652400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:31645400-31653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:31645800-31652600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:31645800-31652800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:31645800-31653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:31646000-31655200	Weak transcription	A549	lung
13	chr15:31646000-31659800	Weak transcription	Fetal Kidney	kidney
14	chr15:31646200-31655600	Enhancers	Right Ventricle	heart
15	chr15:31646200-31657400	Enhancers	Brain Anterior Caudate	brain
16	chr15:31646400-31651800	Weak transcription	K562	blood
17	chr15:31646400-31653000	Weak transcription	HMEC	breast
18	chr15:31646400-31653400	Weak transcription	Aorta	Aorta
19	chr15:31646400-31655000	Enhancers	Fetal Heart	heart
20	chr15:31646400-31657400	Enhancers	Brain Cingulate Gyrus	brain
21	chr15:31646600-31651800	Strong transcription	Fetal Stomach	stomach
22	chr15:31646600-31652000	Weak transcription	Placenta	Placenta
23	chr15:31646600-31652800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:31646600-31653200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:31646600-31653600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:31646600-31656800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr15:31646600-31657400	Weak transcription	HSMMtube	muscle
28	chr15:31646600-31657600	Weak transcription	HSMM	muscle
29	chr15:31646600-31658000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:31647600-31653000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:31647600-31653000	Weak transcription	Hela-S3	cervix
32	chr15:31647600-31654200	Enhancers	Brain Germinal Matrix	brain
33	chr15:31647600-31655600	Enhancers	Pancreas	Pancrea
34	chr15:31647600-31660800	Enhancers	Lung	lung
35	chr15:31648000-31653000	Enhancers	Brain Hippocampus Middle	brain
36	chr15:31648000-31660200	Enhancers	Stomach Mucosa	stomach
37	chr15:31648200-31652200	Enhancers	Spleen	Spleen
38	chr15:31648600-31652000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr15:31648800-31652600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
40	chr15:31649000-31652000	Genic enhancers	Duodenum Mucosa	Duodenum
41	chr15:31649200-31652000	Genic enhancers	Dnd41	blood
42	chr15:31649200-31652400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:31649200-31652600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:31649600-31651800	Genic enhancers	GM12878-XiMat	blood
45	chr15:31649600-31653000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:31649600-31654400	Enhancers	Esophagus	oesophagus
47	chr15:31649800-31651800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:31649800-31651800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:31649800-31652000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr15:31649800-31652000	Weak transcription	Rectal Smooth Muscle	rectum

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