Variant report

Variant	rs16929860
Chromosome Location	chr12:26152384-26152385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10505989	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs10842654	1.00[CEU][hapmap]
rs12425863	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12426668	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1495649	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16929681	0.83[GIH][hapmap]
rs16929780	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16929815	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16929857	0.84[AMR][1000 genomes]
rs16929894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16929895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16929904	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16929970	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs16929998	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2137550	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2343200	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669565	0.92[JPT][hapmap]
rs2669566	0.92[JPT][hapmap]
rs2669568	0.96[CHD][hapmap];0.83[JPT][hapmap]
rs2729626	0.92[JPT][hapmap]
rs2729638	0.82[JPT][hapmap]
rs2729643	0.86[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap]
rs2729644	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2729649	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs3803008	0.84[AMR][1000 genomes]
rs4963643	0.91[AMR][1000 genomes]
rs4963644	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4963947	0.87[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4963952	0.92[JPT][hapmap]
rs57082706	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57791860	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61123975	0.81[AMR][1000 genomes]
rs6487526	0.83[JPT][hapmap]
rs73074872	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73074898	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73077103	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73077131	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077161	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73077176	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73077179	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73079010	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73079023	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73079024	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73079069	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73080925	0.81[AMR][1000 genomes]
rs7961722	0.92[JPT][hapmap]
rs9804876	1.00[CEU][hapmap];0.93[MEX][hapmap];0.83[AMR][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	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16929860	ST8SIA1	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26139600-26160000	Weak transcription	Pancreas	Pancrea
2	chr12:26142200-26155600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:26145200-26152600	Enhancers	Osteobl	bone
4	chr12:26145600-26163000	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:26145800-26152400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:26145800-26153400	Weak transcription	Right Atrium	heart
7	chr12:26146200-26163000	Weak transcription	Lung	lung
8	chr12:26146600-26155600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:26148000-26163600	Weak transcription	Aorta	Aorta
10	chr12:26148200-26155600	Weak transcription	Ovary	ovary
11	chr12:26148200-26157000	Weak transcription	Psoas Muscle	Psoas
12	chr12:26149000-26152600	Weak transcription	Fetal Intestine Small	intestine
13	chr12:26150800-26155600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:26150800-26155600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:26150800-26159600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:26150800-26160000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:26150800-26163200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:26151000-26152600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:26151000-26152800	Weak transcription	HSMMtube	muscle
20	chr12:26151000-26154800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:26151000-26155600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:26151000-26155600	Weak transcription	Fetal Lung	lung
23	chr12:26151000-26155600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:26151000-26155800	Weak transcription	Fetal Heart	heart
25	chr12:26151000-26163000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:26151200-26152800	Enhancers	HUVEC	blood vessel
27	chr12:26151200-26153200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:26151200-26154600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:26151200-26155600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:26151200-26155600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:26151200-26155600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:26151200-26156000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:26151200-26156000	Weak transcription	Brain Anterior Caudate	brain
34	chr12:26151200-26160000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:26151400-26152800	Genic enhancers	NHDF-Ad	bronchial
36	chr12:26151400-26155400	Weak transcription	NHEK	skin
37	chr12:26151400-26156000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:26151400-26160400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:26151400-26162000	Weak transcription	Hela-S3	cervix
40	chr12:26151600-26152600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:26151600-26153600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:26151600-26153800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:26151600-26155600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:26151600-26155600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:26151600-26155600	Weak transcription	NH-A	brain
46	chr12:26151800-26152400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:26151800-26153800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:26152200-26152400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr12:26152200-26152800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:26152200-26153200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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