Variant report

Variant	rs4767937
Chromosome Location	chr12:121223244-121223245
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10774572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10849791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs11065264	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065284	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065293	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065300	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs11065311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11065324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1151849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11608262	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11611087	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12371178	0.81[AMR][1000 genomes]
rs12579868	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580949	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes]
rs12809299	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12822123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs12824150	0.86[CEU][hapmap]
rs12825746	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12831094	0.82[AMR][1000 genomes]
rs13746	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1467283	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1542859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2015462	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2047568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2062507	0.85[CEU][hapmap]
rs2393717	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2893876	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3213567	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3213570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34076777	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35706672	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809313	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3842985	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3861797	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3883901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3897746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3901854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4454799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4766979	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4766980	0.81[AMR][1000 genomes]
rs4767935	0.85[CEU][hapmap]
rs494632	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs520753	0.92[CHB][hapmap]
rs525425	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs534415	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572016	0.81[ASN][1000 genomes]
rs577961	0.81[ASN][1000 genomes]
rs580240	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58291418	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs590625	0.81[ASN][1000 genomes]
rs608394	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs618482	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs668622	0.94[ASN][1000 genomes]
rs7137504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305849	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73413868	0.81[AMR][1000 genomes]
rs7969140	0.81[AMR][1000 genomes]
rs869781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs909053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs989987	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4767937	SPPL3	cis	Nerve Tibial	GTEx
rs4767937	ACADS	cis	Thyroid	GTEx
rs4767937	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs4767937	SPPL3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121206200-121238600	Weak transcription	Small Intestine	intestine
2	chr12:121207000-121223800	Weak transcription	Pancreas	Pancrea
3	chr12:121207200-121225000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:121207200-121226200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:121207200-121233000	Weak transcription	HSMMtube	muscle
6	chr12:121209200-121224200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:121209400-121236800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:121209800-121223400	Strong transcription	Fetal Thymus	thymus
9	chr12:121211400-121260800	Weak transcription	Gastric	stomach
10	chr12:121212600-121229600	Weak transcription	Right Atrium	heart
11	chr12:121212600-121229800	Weak transcription	Right Ventricle	heart
12	chr12:121212600-121236600	Weak transcription	Fetal Heart	heart
13	chr12:121212800-121228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:121213200-121231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:121213400-121224800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:121215000-121224200	Weak transcription	Brain Substantia Nigra	brain
17	chr12:121220600-121223600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:121220600-121225200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:121221000-121225600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:121221000-121227800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:121221000-121250000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:121221200-121223400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:121221200-121223600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:121221200-121223800	Weak transcription	K562	blood
25	chr12:121221200-121226200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:121221200-121226400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:121221200-121229600	Weak transcription	Osteobl	bone
28	chr12:121221200-121233000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:121221200-121233600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:121221200-121249400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:121221400-121224200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:121221400-121225600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:121221400-121228200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:121221400-121229800	Weak transcription	NHDF-Ad	bronchial
35	chr12:121221400-121230400	Weak transcription	HMEC	breast
36	chr12:121221400-121231000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:121221400-121232800	Weak transcription	A549	lung
38	chr12:121221400-121235800	Weak transcription	Hela-S3	cervix
39	chr12:121221400-121240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:121221600-121238800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr12:121222000-121224400	Weak transcription	Brain Germinal Matrix	brain
42	chr12:121222000-121227800	Weak transcription	Fetal Intestine Small	intestine
43	chr12:121222000-121229400	Weak transcription	Brain Anterior Caudate	brain
44	chr12:121222000-121233200	Weak transcription	NHEK	skin
45	chr12:121222000-121233800	Weak transcription	Fetal Stomach	stomach
46	chr12:121222200-121223600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:121222200-121225200	Weak transcription	Psoas Muscle	Psoas
48	chr12:121222200-121225600	Weak transcription	Left Ventricle	heart
49	chr12:121222200-121225800	Weak transcription	Fetal Lung	lung
50	chr12:121222200-121227800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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