Variant report

Variant	rs12354674
Chromosome Location	chr10:26845199-26845200
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10764633	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829019	0.82[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10829020	0.87[ASN][1000 genomes]
rs10829024	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11015154	0.83[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015155	0.83[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015156	0.83[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015160	1.00[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11015161	0.87[CEU][hapmap]
rs11015162	0.95[ASN][1000 genomes]
rs11015163	0.95[ASN][1000 genomes]
rs11015175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11597181	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12355051	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357356	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs67278705	0.95[ASN][1000 genomes]
rs7081291	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096433	0.83[CEU][hapmap]
rs7096704	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766676	0.80[MKK][hapmap]
rs7899859	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7903201	0.83[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7910019	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12354674	PRTFDC1	cis	cerebellum	SCAN
rs12354674	ARMC3	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26802200-26853400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:26834800-26858400	Strong transcription	Dnd41	blood
3	chr10:26839200-26847000	Strong transcription	Primary T helper cells PMA-I stimulated	--
4	chr10:26839400-26854200	Strong transcription	Primary T cells from cord blood	blood
5	chr10:26839600-26860800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr10:26839800-26861200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr10:26840000-26850600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr10:26840000-26860000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr10:26840200-26855200	Weak transcription	Placenta	Placenta
10	chr10:26840200-26863200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:26840400-26849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:26840600-26845600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:26841800-26846000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:26843200-26846400	Genic enhancers	Fetal Thymus	thymus
15	chr10:26843200-26849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:26843200-26849000	Weak transcription	Spleen	Spleen
17	chr10:26843200-26849600	Weak transcription	Lung	lung
18	chr10:26843400-26846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr10:26843600-26845200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr10:26844200-26845200	Weak transcription	GM12878-XiMat	blood
21	chr10:26844200-26846200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr10:26844200-26846200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr10:26844200-26847000	Enhancers	Liver	Liver
24	chr10:26844400-26845600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:26844400-26845800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:26844400-26846000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr10:26844400-26846000	Enhancers	Fetal Intestine Large	intestine
28	chr10:26844400-26846000	Enhancers	Fetal Intestine Small	intestine
29	chr10:26844400-26846200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:26844400-26846200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr10:26844400-26846200	Enhancers	A549	lung
32	chr10:26844400-26846600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr10:26844600-26845200	Enhancers	Pancreas	Pancrea
34	chr10:26844600-26845200	Genic enhancers	Thymus	Thymus
35	chr10:26844600-26845600	Weak transcription	Brain Germinal Matrix	brain
36	chr10:26844600-26845800	Enhancers	Fetal Lung	lung
37	chr10:26844600-26846200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:26844600-26846200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:26844600-26846200	Enhancers	Osteobl	bone
40	chr10:26844600-26846600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr10:26844600-26846600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr10:26844600-26846800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr10:26844600-26847000	Enhancers	Adipose Nuclei	Adipose
44	chr10:26844600-26849000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr10:26844800-26845200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:26844800-26845200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr10:26844800-26845400	Flanking Active TSS	Hela-S3	cervix
48	chr10:26844800-26845600	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr10:26844800-26845600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr10:26844800-26845800	Weak transcription	Right Atrium	heart

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