Variant report

Variant	rs16940651
Chromosome Location	chr15:58937475-58937476
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10851639	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11071391	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11071392	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071393	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11071397	0.84[GIH][hapmap]
rs12437457	0.94[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12437998	0.83[AMR][1000 genomes]
rs12438487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12438810	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439189	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12439231	0.88[CEU][hapmap]
rs12439632	0.81[CEU][hapmap]
rs12440246	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441313	0.88[CEU][hapmap]
rs12441912	0.86[CEU][hapmap]
rs12442451	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591291	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591310	0.84[GIH][hapmap]
rs12591543	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592332	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12592750	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594742	1.00[CEU][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12708455	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901989	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12905110	0.94[CEU][hapmap]
rs12905173	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906705	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906714	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12907237	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908165	0.94[CEU][hapmap];0.82[GIH][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12908261	0.88[CEU][hapmap]
rs12908449	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912286	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12912327	0.83[AMR][1000 genomes]
rs12913383	0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs12915950	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916010	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12917500	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12917577	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1365772	0.80[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1426652	0.87[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs1551445	0.84[GIH][hapmap]
rs16940587	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16940589	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16940647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236194	0.88[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs17301864	0.82[CEU][hapmap]
rs17301905	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1820548	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1869133	0.86[JPT][hapmap]
rs1869135	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2052804	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2052805	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs2081703	0.80[ASN][1000 genomes]
rs2303532	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305421	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28417700	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28455654	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28457680	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28542491	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28573205	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28584993	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28600144	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28609304	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28637832	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28639679	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28678478	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28722857	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28724298	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28728383	0.83[EUR][1000 genomes]
rs28734088	0.81[EUR][1000 genomes]
rs28852159	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34793995	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35499736	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3764196	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4775084	0.81[ASN][1000 genomes]
rs6074	0.82[CEU][hapmap]
rs6494030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6494031	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6494032	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494033	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6494034	0.88[CEU][hapmap]
rs6494038	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs7163733	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164620	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7165035	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7165259	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7165402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166325	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7167528	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169205	0.84[GIH][hapmap]
rs7170314	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7174175	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174414	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178954	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7180550	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026668	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029301	0.81[GIH][hapmap]
rs8029805	0.88[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs8033565	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033691	0.88[CEU][hapmap]
rs8035960	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8036005	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039791	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040358	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9302203	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9635351	0.94[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9744518	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920042	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920310	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9920720	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9921024	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv569602	chr15:58914326-58964437	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16940651	PIGB	cis	cerebellum	SCAN
rs16940651	RNF111	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
3	chr15:58905400-58971800	Weak transcription	Spleen	Spleen
4	chr15:58905600-58976400	Weak transcription	Gastric	stomach
5	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
6	chr15:58907800-58952000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:58911600-58951200	Weak transcription	Fetal Brain Male	brain
8	chr15:58911600-58958000	Weak transcription	Fetal Brain Female	brain
9	chr15:58914200-58957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:58914600-58957000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:58917000-58959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:58919800-58959200	Weak transcription	Brain Germinal Matrix	brain
13	chr15:58920200-58946600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:58920200-58957200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:58921000-58957600	Weak transcription	Colonic Mucosa	Colon
16	chr15:58921200-58946400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:58921200-58946600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:58921200-58946800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:58921200-58949400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:58921200-58959600	Weak transcription	Aorta	Aorta
21	chr15:58921200-58968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:58921600-58942400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:58921600-58946600	Weak transcription	Fetal Intestine Small	intestine
24	chr15:58921600-58959200	Weak transcription	NHLF	lung
25	chr15:58921600-58976600	Weak transcription	Right Ventricle	heart
26	chr15:58921800-58946400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:58921800-58947200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:58921800-58970400	Weak transcription	Stomach Mucosa	stomach
29	chr15:58922200-58939000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr15:58922200-58959000	Weak transcription	HUVEC	blood vessel
31	chr15:58922400-58942600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:58923400-58942400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:58923400-58971800	Weak transcription	Pancreas	Pancrea
34	chr15:58923400-58982800	Weak transcription	Lung	lung
35	chr15:58923800-58947400	Weak transcription	Fetal Stomach	stomach
36	chr15:58924000-58938200	Strong transcription	Fetal Thymus	thymus
37	chr15:58924000-58960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:58926400-58957600	Weak transcription	Brain Substantia Nigra	brain
39	chr15:58927000-58956600	Weak transcription	Ovary	ovary
40	chr15:58927200-58940600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:58927600-58938400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:58927600-58939000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:58928200-58938000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:58928200-58941200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr15:58928600-58937800	Strong transcription	HSMM	muscle
46	chr15:58928800-58938200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:58928800-58938200	Strong transcription	Liver	Liver
48	chr15:58928800-58938400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:58928800-58939600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:58929000-58937800	Strong transcription	Dnd41	blood

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