Variant report

Variant	rs12366527
Chromosome Location	chr12:29474256-29474257
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1035604	0.80[ASN][1000 genomes]
rs1052583	0.84[AFR][1000 genomes]
rs10843366	0.86[ASN][1000 genomes]
rs10843367	0.86[ASN][1000 genomes]
rs10843371	0.89[ASN][1000 genomes]
rs10843377	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843382	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843403	0.91[ASN][1000 genomes]
rs11050152	0.81[ASN][1000 genomes]
rs11050157	0.84[ASN][1000 genomes]
rs11050161	0.88[ASN][1000 genomes]
rs11050162	0.88[ASN][1000 genomes]
rs11050167	0.89[ASN][1000 genomes]
rs11050170	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050173	0.88[ASN][1000 genomes]
rs11050181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050187	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050188	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11050189	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050190	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11050191	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050192	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050193	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11050194	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11050200	0.84[AFR][1000 genomes]
rs11050208	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12228468	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12231498	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12366505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934135	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989478	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1991114	0.80[ASN][1000 genomes]
rs2042511	0.86[ASN][1000 genomes]
rs2194518	0.88[ASN][1000 genomes]
rs2194519	0.89[ASN][1000 genomes]
rs3764953	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782506	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782509	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782511	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4331146	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57803026	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487796	0.89[ASN][1000 genomes]
rs6487801	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6487804	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6487805	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6487808	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67146951	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67517901	0.89[ASN][1000 genomes]
rs7139273	0.81[EUR][1000 genomes]
rs7294598	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7301188	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7302129	0.89[ASN][1000 genomes]
rs7308125	0.89[ASN][1000 genomes]
rs7311912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312164	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737160	0.80[EUR][1000 genomes]
rs7954278	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954871	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957339	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973786	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976961	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962866	0.81[EUR][1000 genomes]
rs9738721	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12366527	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29452800-29494200	Weak transcription	Lung	lung
3	chr12:29453800-29480000	Weak transcription	Gastric	stomach
4	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
5	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
6	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:29459600-29476000	Weak transcription	Fetal Thymus	thymus
8	chr12:29460200-29476000	Weak transcription	Fetal Stomach	stomach
9	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
11	chr12:29463600-29474600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:29463800-29475400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:29464000-29476000	Weak transcription	Fetal Kidney	kidney
14	chr12:29464600-29474800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
16	chr12:29466000-29474400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:29466000-29474600	Weak transcription	Placenta	Placenta
18	chr12:29466200-29488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:29467200-29475800	Weak transcription	Pancreas	Pancrea
20	chr12:29467800-29474600	Weak transcription	Adipose Nuclei	Adipose
21	chr12:29468600-29491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:29469800-29474800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:29470000-29475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:29470000-29475200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:29470000-29475600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:29470000-29475800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:29470000-29486400	Weak transcription	Psoas Muscle	Psoas
28	chr12:29470000-29495600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:29470000-29500000	Weak transcription	K562	blood
30	chr12:29470200-29475000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:29470200-29475200	Weak transcription	Primary T cells from cord blood	blood
32	chr12:29470400-29474600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:29470400-29474800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:29470600-29475200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:29470600-29475400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:29470800-29474400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:29470800-29474600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:29470800-29474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:29470800-29475000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:29470800-29475200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:29470800-29475200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:29470800-29475200	Weak transcription	Dnd41	blood
43	chr12:29470800-29475400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:29470800-29485800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:29470800-29492800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr12:29470800-29492800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:29470800-29493400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:29470800-29493800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:29470800-29496000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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