Variant report

Variant	rs3773820
Chromosome Location	chr3:134083642-134083643
allele	A/C
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:134083001..134085504-chr3:134191468..134193210,2	MCF-7	breast:
2	chr3:134082860..134083688-chr3:134092659..134093845,3	MCF-7	breast:
3	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
4	chr3:134081751..134084258-chr3:134204008..134206303,2	MCF-7	breast:
5	chr3:134081380..134086335-chr3:134201546..134208103,7	MCF-7	breast:
6	chr3:134083461..134085201-chr3:134189189..134191178,2	MCF-7	breast:
7	chr3:134075156..134079286-chr3:134080849..134083812,3	K562	blood:
8	chr3:134083400..134085267-chr3:134166824..134168581,2	MCF-7	breast:
9	chr3:134083418..134085154-chr3:134192940..134194517,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000214289	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000114019	Chromatin interaction
ENSG00000240006	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10755085	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs10755086	0.89[ASN][1000 genomes]
rs1111516	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs11708815	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719057	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12495847	0.85[ASN][1000 genomes]
rs12496438	0.89[ASN][1000 genomes]
rs13075185	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322269	0.89[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs1353776	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1353777	0.85[ASN][1000 genomes]
rs1353778	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1466827	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1498731	0.90[ASN][1000 genomes]
rs1603824	0.90[ASN][1000 genomes]
rs1863910	0.85[ASN][1000 genomes]
rs2133307	0.90[ASN][1000 genomes]
rs2303635	0.88[CHB][hapmap]
rs2400278	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2400279	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2400280	0.83[ASN][1000 genomes]
rs34341902	0.90[ASN][1000 genomes]
rs35951257	0.90[ASN][1000 genomes]
rs3732852	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3755762	0.89[ASN][1000 genomes]
rs3821705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4974485	0.90[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974489	0.86[ASN][1000 genomes]
rs4974491	0.86[ASN][1000 genomes]
rs4974494	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4974495	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4974496	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs4974497	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4974498	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6439477	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs6439478	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6786148	0.86[ASN][1000 genomes]
rs7613066	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9817900	0.86[ASN][1000 genomes]
rs9853621	0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3773820	RP11-375I20.6	cis	Artery Tibial	GTEx
rs3773820	TMEM22	cis	parietal	SCAN
rs3773820	RP11-375I20.6	cis	Thyroid	GTEx
rs3773820	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs3773820	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs3773820	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs3773820	FOXL2	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134069200-134090000	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr3:134069400-134089800	Genic enhancers	Fetal Muscle Leg	muscle
3	chr3:134070400-134088200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:134071000-134088800	Enhancers	Right Atrium	heart
5	chr3:134072200-134090200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
7	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
8	chr3:134073000-134089400	Genic enhancers	HMEC	breast
9	chr3:134073400-134091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:134074400-134089400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:134075000-134090400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:134076800-134088600	Genic enhancers	NHDF-Ad	bronchial
13	chr3:134077600-134088000	Genic enhancers	NH-A	brain
14	chr3:134078800-134090400	Genic enhancers	Liver	Liver
15	chr3:134079200-134083800	Strong transcription	HepG2	liver
16	chr3:134079400-134089600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:134080400-134084600	Genic enhancers	Esophagus	oesophagus
18	chr3:134081400-134084800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:134081400-134085000	Genic enhancers	Fetal Kidney	kidney
20	chr3:134081400-134090600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:134081600-134084800	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:134081600-134091000	Enhancers	Psoas Muscle	Psoas
23	chr3:134082000-134084000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
24	chr3:134082000-134084200	Genic enhancers	Pancreas	Pancrea
25	chr3:134082000-134084400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
26	chr3:134082000-134086800	Genic enhancers	Fetal Lung	lung
27	chr3:134082000-134089800	Genic enhancers	Placenta Amnion	Placenta Amnion
28	chr3:134082000-134090800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:134082000-134090800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:134082000-134091000	Genic enhancers	Fetal Stomach	stomach
31	chr3:134082200-134083800	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
32	chr3:134082200-134084200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:134082200-134084200	Enhancers	Fetal Brain Male	brain
34	chr3:134082200-134084600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr3:134082200-134090200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:134082200-134092800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:134082400-134083800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr3:134082400-134084000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr3:134082400-134084000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:134082400-134084000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr3:134082400-134084000	Flanking Active TSS	Dnd41	blood
42	chr3:134082400-134084200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
43	chr3:134082400-134084400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
44	chr3:134082400-134085200	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
45	chr3:134082400-134091400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:134082600-134083800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr3:134082600-134083800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:134082600-134083800	Flanking Active TSS	Colonic Mucosa	Colon
49	chr3:134082600-134084000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:134082600-134084000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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