Variant report

Variant	rs3806705
Chromosome Location	chr3:46608274-46608275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:46607267-46608300	IMR90	lung:	n/a	n/a
2	TCF12	chr3:46607448-46608364	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr3:46606816-46608527	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr3:46607548-46608326	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr3:46608140-46608353	SH-SY5Y	brain:	n/a	chr3:46608179-46608200
6	NFIC	chr3:46607587-46608356	SK-N-SH	brain:	n/a	n/a
7	EP300	chr3:46607027-46608631	SK-N-SH	brain:	n/a	chr3:46608421-46608428 chr3:46607626-46607642
8	JUND	chr3:46607736-46608284	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LRRC2	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1520491	0.83[ASN][1000 genomes]
rs17221605	0.83[ASN][1000 genomes]
rs17287344	0.83[ASN][1000 genomes]
rs56383925	0.83[ASN][1000 genomes]
rs57865489	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs939414	0.83[ASN][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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46606200-46608400	Active TSS	Right Ventricle	heart
2	chr3:46606800-46608400	Active TSS	Ovary	ovary
3	chr3:46607000-46608400	Active TSS	Colon Smooth Muscle	Colon
4	chr3:46607000-46608400	Bivalent Enhancer	Fetal Lung	lung
5	chr3:46607000-46608400	Active TSS	Rectal Smooth Muscle	rectum
6	chr3:46607000-46608400	Active TSS	Right Atrium	heart
7	chr3:46607200-46608400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:46607200-46608400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:46607200-46608400	Active TSS	NHLF	lung
10	chr3:46607200-46608600	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr3:46607400-46608400	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr3:46607600-46608400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:46607600-46608400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:46607800-46608400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:46607800-46608400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:46607800-46608400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
17	chr3:46607800-46608400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr3:46607800-46608400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:46607800-46608400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:46607800-46608400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:46608000-46608400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:46608000-46608400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr3:46608000-46608400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
24	chr3:46608000-46608400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr3:46608000-46608400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr3:46608000-46608400	Flanking Active TSS	Liver	Liver
27	chr3:46608000-46608400	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr3:46608000-46608400	Bivalent Enhancer	Fetal Thymus	thymus
29	chr3:46608000-46608400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr3:46608000-46608400	Flanking Active TSS	HSMMtube	muscle
31	chr3:46608000-46608400	Flanking Active TSS	Osteobl	bone
32	chr3:46608200-46608400	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr3:46608200-46608400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr3:46608200-46608400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:46608200-46608400	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:46608200-46608400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
37	chr3:46608200-46608400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:46608200-46608400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:46608200-46608400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
40	chr3:46608200-46608400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:46608200-46608400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:46608200-46608400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:46608200-46608400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:46608200-46608400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:46608200-46608400	Bivalent Enhancer	Primary T cells from cord blood	blood
46	chr3:46608200-46608400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:46608200-46608400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:46608200-46608400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:46608200-46608400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:46608200-46608400	Enhancers	Brain Cingulate Gyrus	brain

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