Variant report

Variant	rs12916825
Chromosome Location	chr15:77491247-77491248
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10519162	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12898388	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12898812	0.98[EUR][1000 genomes]
rs12899474	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12899826	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12900663	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12901370	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12901861	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12903728	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12905339	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12905361	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12905519	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12908288	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12910127	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12910235	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12910585	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12910671	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12911305	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12911480	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12912053	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12912098	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12912482	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12913049	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12913548	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12915165	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12916044	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12916257	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12916933	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12917081	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12917153	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs14726	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16968677	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16968680	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16968681	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17381898	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17382597	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17383239	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17469938	1.00[CEU][hapmap]
rs33999898	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34113420	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34117936	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34470437	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34479592	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34554116	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34562889	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34568673	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34630840	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34640404	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34828432	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34896181	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35111546	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35258007	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35373370	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35381299	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35477234	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35562610	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35669736	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35704799	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35705080	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35778295	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35833143	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35900967	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35945311	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36043229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62007252	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62007254	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62007257	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62007258	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62008360	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62008378	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62008381	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62008382	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62008383	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62008384	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62008412	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62008416	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62008418	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62008425	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62008433	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62008453	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67683937	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67839374	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12916825	SGK269	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77451200-77491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:77461600-77496800	Weak transcription	Lung	lung
3	chr15:77467200-77491400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:77469800-77499200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:77471400-77505800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:77471800-77491400	Weak transcription	Aorta	Aorta
7	chr15:77472400-77500800	Weak transcription	HSMMtube	muscle
8	chr15:77473600-77527800	Weak transcription	Placenta	Placenta
9	chr15:77476400-77491400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:77479400-77494400	Weak transcription	HepG2	liver
11	chr15:77480400-77492000	Weak transcription	Small Intestine	intestine
12	chr15:77480400-77492000	Weak transcription	Thymus	Thymus
13	chr15:77480400-77528000	Weak transcription	Fetal Stomach	stomach
14	chr15:77481800-77491600	Weak transcription	NHLF	lung
15	chr15:77482000-77506200	Weak transcription	Pancreas	Pancrea
16	chr15:77482200-77491400	Weak transcription	Dnd41	blood
17	chr15:77482200-77493800	Weak transcription	Right Ventricle	heart
18	chr15:77482200-77504800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:77482200-77528000	Weak transcription	Spleen	Spleen
20	chr15:77484000-77518800	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:77487400-77516800	Weak transcription	Fetal Heart	heart
22	chr15:77487800-77491400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:77488400-77491400	Weak transcription	Fetal Kidney	kidney
24	chr15:77488400-77494000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:77488600-77491400	Weak transcription	Fetal Intestine Large	intestine
26	chr15:77488600-77491400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:77488600-77491400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:77488600-77494000	Weak transcription	Brain Angular Gyrus	brain
29	chr15:77488800-77491800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:77489600-77493800	Weak transcription	Fetal Brain Male	brain
31	chr15:77490400-77491600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:77490400-77492400	Strong transcription	Osteobl	bone
33	chr15:77490600-77491400	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr15:77490600-77491600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:77490600-77491800	Strong transcription	Brain Cingulate Gyrus	brain
36	chr15:77490600-77491800	ZNF genes & repeats	Brain Substantia Nigra	brain
37	chr15:77490600-77492000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr15:77490600-77492000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
39	chr15:77490600-77492000	Strong transcription	HUVEC	blood vessel
40	chr15:77490600-77492200	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr15:77490600-77492200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:77490600-77492200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:77490600-77492200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr15:77490600-77492400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:77490600-77492400	Strong transcription	HSMM	muscle
46	chr15:77490600-77492600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr15:77490600-77492800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:77490600-77492800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr15:77490800-77491400	ZNF genes & repeats	Liver	Liver
50	chr15:77490800-77491600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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