Variant report

Variant	rs11720829
Chromosome Location	chr3:42822870-42822871
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42822052..42823428-chr3:42880867..42881869,6	K562	blood:
2	chr3:42822158..42825111-chr3:42859747..42864904,5	MCF-7	breast:
3	chr3:42821670..42822964-chr3:42922020..42923129,17	K562	blood:
4	chr3:42822357..42822898-chr3:42922644..42923160,2	MCF-7	breast:
5	chr3:42821025..42823114-chr3:42833487..42836032,2	MCF-7	breast:
6	chr3:42817217..42818937-chr3:42821351..42822970,2	K562	blood:
7	chr3:42819275..42824150-chr3:42869754..42873104,6	MCF-7	breast:
8	chr3:42821500..42822997-chr3:42871419..42873013,19	K562	blood:
9	chr3:42822783..42824353-chr3:42860030..42861714,2	MCF-7	breast:
10	chr3:42820953..42824187-chr3:42845288..42847864,3	MCF-7	breast:
11	chr3:42821893..42823608-chr3:42825720..42828571,2	K562	blood:
12	chr3:42822059..42823039-chr3:42871468..42872331,5	MCF-7	breast:
13	chr3:42820160..42826427-chr3:42842009..42849039,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000144648	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11129971	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11129973	1.00[ASW][hapmap];0.93[LWK][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11708224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12488173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13062528	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs1564176	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564177	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1991438	0.82[AFR][1000 genomes]
rs339663	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339669	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339673	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339675	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339679	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35426298	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4399859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4404423	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682855	0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683331	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683334	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs5027058	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60959614	0.85[AMR][1000 genomes]
rs6442065	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773636	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6778695	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7610350	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611520	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612614	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612782	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614158	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620291	0.87[AFR][1000 genomes]
rs7648688	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9755640	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9862147	0.85[AMR][1000 genomes]
rs9866005	0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882356	0.85[AMR][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	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42814800-42823800	Weak transcription	Lung	lung
2	chr3:42814800-42824800	Weak transcription	Gastric	stomach
3	chr3:42814800-42840800	Weak transcription	Spleen	Spleen
4	chr3:42815000-42823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:42815000-42824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:42815000-42834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:42815200-42823000	Weak transcription	Colonic Mucosa	Colon
8	chr3:42815200-42823600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:42815200-42823600	Weak transcription	Placenta	Placenta
10	chr3:42815200-42823800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:42815200-42823800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:42815200-42823800	Weak transcription	Fetal Brain Female	brain
13	chr3:42815200-42823800	Weak transcription	Left Ventricle	heart
14	chr3:42815200-42823800	Weak transcription	GM12878-XiMat	blood
15	chr3:42815200-42823800	Weak transcription	HMEC	breast
16	chr3:42815200-42824000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:42815200-42824000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:42815200-42824000	Weak transcription	HSMM	muscle
19	chr3:42815200-42824200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:42815200-42824400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:42815200-42824400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:42815200-42824600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:42815200-42824600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:42815200-42824600	Weak transcription	NH-A	brain
25	chr3:42815200-42824800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:42815200-42824800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:42815200-42824800	Weak transcription	Fetal Thymus	thymus
28	chr3:42815200-42827000	Weak transcription	Fetal Lung	lung
29	chr3:42815200-42828200	Weak transcription	Fetal Intestine Small	intestine
30	chr3:42815200-42834800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:42815200-42834800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:42815200-42834800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:42815200-42834800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:42815200-42834800	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:42815200-42834800	Weak transcription	Ovary	ovary
36	chr3:42815200-42834800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:42815200-42834800	Weak transcription	A549	lung
38	chr3:42815200-42835200	Weak transcription	Right Ventricle	heart
39	chr3:42815200-42836400	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:42815200-42837400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:42815200-42842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:42815200-42842200	Weak transcription	Aorta	Aorta
43	chr3:42815200-42842400	Weak transcription	Psoas Muscle	Psoas
44	chr3:42815400-42823600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:42815400-42823600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:42815400-42824000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:42815400-42824400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:42815400-42824600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:42815400-42824600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:42815400-42824600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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