Variant report

Variant	rs28709836
Chromosome Location	chr3:119731254-119731255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119730742..119733006-chr3:119735849..119738068,2	MCF-7	breast:
2	chr3:119729710..119735147-chr3:119812192..119816098,5	MCF-7	breast:
3	chr3:119717638..119719374-chr3:119730328..119732914,2	MCF-7	breast:
4	chr3:119730961..119733403-chr3:119813140..119815565,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12330358	0.88[AFR][1000 genomes]
rs12330670	0.88[AFR][1000 genomes]
rs13315412	0.96[AFR][1000 genomes]
rs13316265	0.89[AFR][1000 genomes]
rs13319151	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs13319559	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs13319825	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs13323804	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs28366921	0.81[AFR][1000 genomes]
rs28481299	0.88[AFR][1000 genomes]
rs28540006	1.00[ASW][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.88[AFR][1000 genomes]
rs28817295	0.96[AFR][1000 genomes]
rs6769820	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6772172	0.87[YRI][hapmap];0.96[AFR][1000 genomes]
rs6778773	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6796719	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7639665	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7639675	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9289137	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9289139	0.92[AFR][1000 genomes]
rs9810851	0.96[AFR][1000 genomes]
rs9816765	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9816864	0.96[AFR][1000 genomes]
rs9819836	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9825770	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9826355	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9831646	1.00[YRI][hapmap]
rs9835672	0.96[AFR][1000 genomes]
rs9836177	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9836325	0.96[AFR][1000 genomes]
rs9837710	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9840111	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9841959	0.96[AFR][1000 genomes]
rs9842216	0.96[AFR][1000 genomes]
rs9842542	0.96[AFR][1000 genomes]
rs9843873	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9852118	0.96[AFR][1000 genomes]
rs9852797	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9854117	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9857139	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9857548	0.96[AFR][1000 genomes]
rs9858471	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9861481	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9862099	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9864153	0.96[AFR][1000 genomes]
rs9869296	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9871701	0.96[AFR][1000 genomes]
rs9871925	0.96[AFR][1000 genomes]
rs9872693	0.96[AFR][1000 genomes]
rs9874110	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9879732	0.83[MKK][hapmap]
rs9880833	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9881985	1.00[YRI][hapmap];0.96[AFR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28709836	OAT	trans	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119693600-119732200	Weak transcription	A549	lung
2	chr3:119712000-119732200	Weak transcription	HepG2	liver
3	chr3:119712200-119732400	Weak transcription	NHLF	lung
4	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
5	chr3:119712800-119732200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
7	chr3:119717600-119732200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:119718200-119736800	Weak transcription	Liver	Liver
9	chr3:119720200-119731800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:119720200-119736600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:119720200-119741000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:119720400-119737200	Weak transcription	NHDF-Ad	bronchial
13	chr3:119720800-119738600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:119721400-119733600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:119723200-119734800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:119723200-119736200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:119723400-119731800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:119723600-119731400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:119723600-119731800	Weak transcription	Right Ventricle	heart
20	chr3:119723600-119740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:119724000-119736800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:119724000-119738200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:119724000-119741400	Weak transcription	Thymus	Thymus
24	chr3:119724200-119734600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:119724400-119731400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:119729200-119732600	Enhancers	Colon Smooth Muscle	Colon
27	chr3:119729800-119732000	Enhancers	Ovary	ovary
28	chr3:119729800-119732000	Enhancers	Psoas Muscle	Psoas
29	chr3:119729800-119733000	Enhancers	Brain Cingulate Gyrus	brain
30	chr3:119729800-119734000	Enhancers	Brain Substantia Nigra	brain
31	chr3:119730000-119743000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:119730000-119743000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:119730400-119732000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:119730400-119732600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:119730600-119731800	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:119730600-119732000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:119730600-119732000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:119730600-119733800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:119730600-119736200	Weak transcription	Stomach Mucosa	stomach
40	chr3:119730600-119736400	Weak transcription	Small Intestine	intestine
41	chr3:119730600-119739200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:119730600-119740800	Weak transcription	Left Ventricle	heart
43	chr3:119730600-119741600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:119730800-119731600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:119730800-119732600	Enhancers	Rectal Smooth Muscle	rectum
46	chr3:119730800-119736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:119731000-119732000	Weak transcription	Brain Anterior Caudate	brain
48	chr3:119731000-119732200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:119731000-119741400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:119731200-119731400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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