Variant report

Variant	rs12385963
Chromosome Location	chr15:55482851-55482852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10162819	0.93[ASN][1000 genomes]
rs10162843	0.93[ASN][1000 genomes]
rs1050931	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10518801	0.81[ASN][1000 genomes]
rs10518804	0.85[ASN][1000 genomes]
rs1061821	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1061822	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1061823	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1061824	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1061870	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1061873	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1061874	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1061875	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11852763	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855907	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855973	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855978	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11856010	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11857087	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13733	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16976036	0.83[ASN][1000 genomes]
rs16976039	0.83[ASN][1000 genomes]
rs16976065	0.87[ASN][1000 genomes]
rs16976083	0.87[ASN][1000 genomes]
rs16976094	0.92[ASN][1000 genomes]
rs16976116	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16976149	0.93[ASN][1000 genomes]
rs28433503	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28449712	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28489312	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28499113	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28508034	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28522816	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28526269	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28530662	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28535372	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28541469	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28558576	0.92[ASN][1000 genomes]
rs28562431	0.93[ASN][1000 genomes]
rs28564077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28589384	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28589609	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28590021	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs28591259	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28592928	0.86[ASN][1000 genomes]
rs28600759	0.83[ASN][1000 genomes]
rs28630909	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28636526	0.85[ASN][1000 genomes]
rs28649719	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28673043	0.82[ASN][1000 genomes]
rs28699327	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28704109	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28706531	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28708989	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28710976	1.00[ASN][1000 genomes]
rs28714578	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28784096	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28864456	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28889339	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2899580	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2899581	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2899582	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3179664	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3759861	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759862	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809539	0.89[ASN][1000 genomes]
rs3809540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4238316	0.92[ASN][1000 genomes]
rs4503734	0.99[ASN][1000 genomes]
rs4545742	0.90[ASN][1000 genomes]
rs56328329	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62020097	0.85[AFR][1000 genomes]
rs62020114	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493769	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493771	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7165491	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168472	1.00[ASN][1000 genomes]
rs7168737	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7172108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7172289	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7172575	0.81[ASN][1000 genomes]
rs7176676	0.82[ASN][1000 genomes]
rs7179365	0.93[ASN][1000 genomes]
rs7180594	0.93[ASN][1000 genomes]
rs73409851	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73409853	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8027098	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8027256	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8028525	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8030981	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8031949	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8033588	0.93[ASN][1000 genomes]
rs8034063	0.93[ASN][1000 genomes]
rs8034402	1.00[ASN][1000 genomes]
rs8034853	0.93[ASN][1000 genomes]
rs8034882	0.93[ASN][1000 genomes]
rs8035625	1.00[ASN][1000 genomes]
rs8043029	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9920136	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9920219	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9920220	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9920737	0.83[ASN][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	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv525768	chr15:55466155-55485494	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12385963	PIGB	cis	Artery Tibial	GTEx
rs12385963	RAB27A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55455800-55487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:55462600-55488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55464800-55488200	Weak transcription	Lung	lung
4	chr15:55466800-55486800	Weak transcription	Psoas Muscle	Psoas
5	chr15:55468800-55487000	Weak transcription	Gastric	stomach
6	chr15:55469200-55484800	Strong transcription	Liver	Liver
7	chr15:55469200-55485000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr15:55469400-55485200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:55469600-55485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:55469600-55485200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:55469600-55486000	Strong transcription	Primary B cells from cord blood	blood
12	chr15:55469800-55484800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:55469800-55485000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:55469800-55486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:55469800-55486600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:55470000-55484800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr15:55470000-55484800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:55470200-55484000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:55470200-55486600	Weak transcription	Small Intestine	intestine
20	chr15:55470400-55485000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:55470400-55485200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:55470400-55486400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr15:55470400-55486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:55470800-55485800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:55471000-55484800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:55471000-55485000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:55471000-55486000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:55471000-55486200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:55471000-55487000	Weak transcription	Pancreas	Pancrea
30	chr15:55471400-55485800	Weak transcription	Stomach Mucosa	stomach
31	chr15:55471600-55486800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:55472000-55484800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:55472000-55485000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:55472000-55486200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:55472200-55488000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:55472400-55488400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:55472600-55488400	Weak transcription	Esophagus	oesophagus
38	chr15:55473000-55487000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:55473000-55487400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:55473000-55487600	Weak transcription	Aorta	Aorta
41	chr15:55473600-55486800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:55474200-55486200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:55475000-55487400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr15:55475200-55484000	Weak transcription	NHLF	lung
45	chr15:55475800-55484000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:55476000-55483800	Weak transcription	HSMMtube	muscle
47	chr15:55476400-55483400	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:55476600-55485600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr15:55477000-55484000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:55477200-55483400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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