Variant report

Variant	rs9874110
Chromosome Location	chr3:119558349-119558350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119553090..119555920-chr3:119558108..119560664,3	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12330290	0.88[AFR][1000 genomes]
rs12330358	1.00[AFR][1000 genomes]
rs12330670	1.00[AFR][1000 genomes]
rs13315412	0.92[AFR][1000 genomes]
rs13316265	0.85[AFR][1000 genomes]
rs13319151	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs13319559	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs13319825	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs13323804	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs28366921	0.92[AFR][1000 genomes]
rs28481299	1.00[AFR][1000 genomes]
rs28540006	1.00[ASW][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];1.00[AFR][1000 genomes]
rs28709836	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs28817295	0.92[AFR][1000 genomes]
rs6769820	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6772172	0.87[YRI][hapmap];0.92[AFR][1000 genomes]
rs6778773	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6796719	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7639665	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7639675	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9289137	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9810851	0.92[AFR][1000 genomes]
rs9816765	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9819836	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9825770	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9826355	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9831646	1.00[YRI][hapmap]
rs9835672	0.92[AFR][1000 genomes]
rs9836177	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9837710	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9841959	0.92[AFR][1000 genomes]
rs9842542	0.92[AFR][1000 genomes]
rs9843873	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9852118	0.92[AFR][1000 genomes]
rs9852797	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9854117	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9857139	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9857548	0.92[AFR][1000 genomes]
rs9858471	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9861481	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9864153	0.92[AFR][1000 genomes]
rs9864678	0.83[AFR][1000 genomes]
rs9869296	1.00[YRI][hapmap]
rs9871701	0.92[AFR][1000 genomes]
rs9871925	0.92[AFR][1000 genomes]
rs9872693	0.92[AFR][1000 genomes]
rs9880833	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9881985	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9990259	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9874110	OAT	trans	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
3	chr3:119534800-119558600	Weak transcription	Colonic Mucosa	Colon
4	chr3:119536200-119569000	Weak transcription	Esophagus	oesophagus
5	chr3:119536400-119570200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:119536600-119576000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:119536600-119576400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:119539000-119576400	Weak transcription	Ovary	ovary
9	chr3:119540400-119563600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:119540400-119574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:119540400-119576600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:119540800-119577000	Weak transcription	Aorta	Aorta
13	chr3:119541000-119581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:119541200-119561800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:119541200-119587000	Weak transcription	Gastric	stomach
16	chr3:119541800-119559200	Weak transcription	Pancreas	Pancrea
17	chr3:119541800-119560000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:119542400-119581200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:119542600-119560800	Weak transcription	Hela-S3	cervix
20	chr3:119542600-119581600	Weak transcription	HUVEC	blood vessel
21	chr3:119542800-119575000	Weak transcription	Fetal Kidney	kidney
22	chr3:119544000-119561800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:119545000-119559600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:119545000-119576400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:119545200-119559200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:119545200-119559400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:119545200-119561600	Weak transcription	Fetal Stomach	stomach
28	chr3:119545200-119562800	Weak transcription	NHLF	lung
29	chr3:119545200-119575000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:119545200-119575000	Weak transcription	Adipose Nuclei	Adipose
31	chr3:119545200-119575400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:119545200-119583400	Weak transcription	Brain Angular Gyrus	brain
33	chr3:119545800-119560400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:119545800-119576400	Weak transcription	Brain Germinal Matrix	brain
35	chr3:119545800-119581600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:119546000-119561800	Weak transcription	Left Ventricle	heart
37	chr3:119546000-119561800	Weak transcription	Thymus	Thymus
38	chr3:119546000-119569000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:119546000-119571800	Weak transcription	GM12878-XiMat	blood
40	chr3:119546000-119575000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:119546000-119576400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:119546000-119663400	Weak transcription	Lung	lung
43	chr3:119546200-119559400	Weak transcription	Fetal Thymus	thymus
44	chr3:119546200-119561400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:119546200-119569000	Weak transcription	Placenta	Placenta
46	chr3:119546200-119575000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:119546400-119567000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:119546400-119575200	Weak transcription	Liver	Liver
49	chr3:119546400-119580400	Weak transcription	HepG2	liver
50	chr3:119547600-119560400	Weak transcription	Primary T cells fromperipheralblood	blood

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