Variant report

Variant	rs10887885
Chromosome Location	chr10:90785260-90785261
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10788628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10887876	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs10887878	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10887886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202922	1.00[CEU][hapmap]
rs11202926	0.97[ASN][1000 genomes]
rs11202928	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202931	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1159120	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1324551	0.80[JPT][hapmap]
rs1468063	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1810763	0.83[ASN][1000 genomes]
rs2147418	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296601	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296602	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296604	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2862830	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2862831	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2862832	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2862833	0.82[ASN][1000 genomes]
rs35150762	0.82[ASN][1000 genomes]
rs3752985	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4934433	0.82[JPT][hapmap]
rs6586160	0.82[JPT][hapmap]
rs6586161	0.86[JPT][hapmap]
rs7097467	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs7896789	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7911226	0.88[ASN][1000 genomes]
rs7914779	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7915235	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7920305	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs874144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874145	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9325603	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs9658767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9658769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9658773	0.82[YRI][hapmap]
rs982764	0.88[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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10887885	ACTA2	cis	lymphoblastoid	seeQTL
rs10887885	ACTA2	cis	multi-tissue	Pritchard
rs10887885	FAS	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90754000-90789600	Weak transcription	A549	lung
2	chr10:90761800-90786200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr10:90762400-90785800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:90762600-90786000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:90766200-90785600	Strong transcription	GM12878-XiMat	blood
6	chr10:90767600-90786600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr10:90771600-90789600	Weak transcription	Brain Anterior Caudate	brain
8	chr10:90771800-90808600	Weak transcription	Primary T cells from cord blood	blood
9	chr10:90772400-90795000	Weak transcription	Placenta	Placenta
10	chr10:90772600-90789600	Weak transcription	Fetal Stomach	stomach
11	chr10:90772600-90791800	Weak transcription	Esophagus	oesophagus
12	chr10:90772600-90792000	Weak transcription	Colonic Mucosa	Colon
13	chr10:90772600-90795800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:90775000-90789400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr10:90775200-90789400	Weak transcription	NH-A	brain
16	chr10:90776200-90789400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr10:90776600-90792600	Weak transcription	Right Ventricle	heart
18	chr10:90776800-90789400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr10:90778000-90791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr10:90779200-90791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:90780200-90791400	Weak transcription	Spleen	Spleen
22	chr10:90780400-90786400	Weak transcription	Fetal Brain Male	brain
23	chr10:90780400-90789600	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:90780400-90790600	Weak transcription	Hela-S3	cervix
25	chr10:90780600-90786400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr10:90780600-90789400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:90780600-90789400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:90780600-90789400	Weak transcription	Adipose Nuclei	Adipose
29	chr10:90780600-90789600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr10:90780600-90789600	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:90780600-90789600	Weak transcription	Left Ventricle	heart
32	chr10:90780600-90789800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr10:90780600-90791000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr10:90780600-90791800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr10:90780600-90791800	Weak transcription	HSMM	muscle
36	chr10:90780600-90792000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:90780600-90792400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr10:90780800-90786200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr10:90780800-90791800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:90780800-90804200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr10:90781000-90786600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr10:90781000-90788800	Weak transcription	Fetal Lung	lung
43	chr10:90781000-90789400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr10:90781000-90789600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr10:90781000-90790800	Weak transcription	Lung	lung
46	chr10:90781000-90791600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:90781000-90791800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr10:90781200-90791800	Weak transcription	Fetal Thymus	thymus
49	chr10:90781400-90790600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr10:90781600-90788600	Weak transcription	Ovary	ovary

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