Variant report

Variant	rs12439686
Chromosome Location	chr15:31559529-31559530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10438322	0.89[ASN][1000 genomes]
rs12101670	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12323980	0.82[ASN][1000 genomes]
rs12437996	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1370062	0.89[ASN][1000 genomes]
rs1972825	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28451043	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28631253	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28669757	0.86[ASN][1000 genomes]
rs3743235	0.86[ASN][1000 genomes]
rs6493531	0.89[ASN][1000 genomes]
rs7162278	0.86[ASN][1000 genomes]
rs7162751	0.83[ASN][1000 genomes]
rs73381204	0.81[ASN][1000 genomes]
rs754611	0.86[ASN][1000 genomes]
rs9944280	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription 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	52 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv903839	chr15:31495113-31576677	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	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
12	nsv456747	chr15:31537496-31637996	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv568772	chr15:31537496-31637996	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12439686	GOLGA8R	cis	Heart Left Ventricle	GTEx
rs12439686	RP11-932O9.9	cis	Esophagus Muscularis	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31550600-31567600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:31553200-31561800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:31553400-31561400	Enhancers	Primary B cells from peripheral blood	blood
4	chr15:31553400-31563600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr15:31553600-31560000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:31553600-31560800	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:31553600-31560800	Enhancers	Brain Hippocampus Middle	brain
8	chr15:31553600-31561400	Enhancers	Fetal Muscle Leg	muscle
9	chr15:31554400-31561400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:31554800-31560400	Enhancers	Liver	Liver
11	chr15:31554800-31561000	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr15:31555000-31563600	Enhancers	Adipose Nuclei	Adipose
13	chr15:31555000-31565000	Enhancers	Fetal Heart	heart
14	chr15:31555200-31561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:31555200-31561000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr15:31555400-31559600	Enhancers	Brain Cingulate Gyrus	brain
17	chr15:31555400-31560800	Enhancers	Stomach Mucosa	stomach
18	chr15:31555400-31563400	Enhancers	Fetal Intestine Small	intestine
19	chr15:31555600-31561600	Enhancers	HSMMtube	muscle
20	chr15:31555800-31559600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr15:31555800-31560200	Enhancers	Brain Substantia Nigra	brain
22	chr15:31556200-31560000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:31556400-31559800	Enhancers	Spleen	Spleen
24	chr15:31556400-31560800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr15:31556600-31560200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr15:31556600-31568200	Enhancers	Placenta	Placenta
27	chr15:31556800-31567400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:31556800-31567600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:31557000-31559600	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:31557000-31559800	Flanking Active TSS	Dnd41	blood
31	chr15:31557400-31559600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:31557600-31564400	Weak transcription	Fetal Brain Male	brain
33	chr15:31557800-31560200	Enhancers	HSMM	muscle
34	chr15:31558000-31560400	Enhancers	Brain Angular Gyrus	brain
35	chr15:31558000-31562400	Enhancers	Colonic Mucosa	Colon
36	chr15:31558200-31559600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr15:31558200-31559600	Weak transcription	Gastric	stomach
38	chr15:31558200-31559800	Weak transcription	Esophagus	oesophagus
39	chr15:31558200-31562800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:31558400-31560200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:31558400-31560400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:31558400-31565800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:31558400-31567400	Weak transcription	Pancreas	Pancrea
44	chr15:31558600-31562400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:31558800-31559800	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr15:31558800-31559800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr15:31558800-31560400	Enhancers	Lung	lung
48	chr15:31558800-31561000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr15:31559000-31559600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:31559000-31559600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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