Variant report

Variant	rs66509404
Chromosome Location	chr3:155590230-155590231
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:155520264..155525290-chr3:155586627..155590296,8	K562	blood:
2	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:
3	chr3:155461523..155464397-chr3:155587900..155591398,5	MCF-7	breast:
4	chr3:155568718..155574348-chr3:155586235..155593210,15	K562	blood:
5	chr3:155546434..155549740-chr3:155588922..155591609,3	K562	blood:
6	chr3:155522036..155526613-chr3:155586597..155592084,8	K562	blood:
7	chr3:155570444..155573449-chr3:155586982..155591161,10	MCF-7	breast:
8	chr3:155508129..155511910-chr3:155589025..155592150,5	K562	blood:
9	chr20:52490662..52493657-chr3:155587949..155590436,2	MCF-7	breast:
10	chr3:155542984..155546032-chr3:155588634..155590406,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174928	Chromatin interaction
ENSG00000169359	Chromatin interaction
ENSG00000114805	Chromatin interaction
ENSG00000214919	Chromatin interaction
ENSG00000241721	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10804773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804774	0.92[ASN][1000 genomes]
rs10936020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1131925	0.89[ASN][1000 genomes]
rs11714133	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13059611	0.90[ASN][1000 genomes]
rs13091683	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13096499	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2054878	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2063903	0.93[ASN][1000 genomes]
rs34337666	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35321137	0.92[ASN][1000 genomes]
rs35472369	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs358703	0.82[AMR][1000 genomes]
rs3772115	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772116	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821365	0.97[ASN][1000 genomes]
rs4680219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680223	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55662848	0.81[EUR][1000 genomes]
rs6441028	0.97[ASN][1000 genomes]
rs6763830	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6799267	0.96[ASN][1000 genomes]
rs6809229	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7619976	0.99[ASN][1000 genomes]
rs7633168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7643630	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7651038	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7652005	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv877681	chr3:155535670-155654017	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3325134	chr3:155587683-155590231	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 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	chr3:155587400-155590600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:155587400-155590600	Active TSS	HepG2	liver
3	chr3:155587400-155591000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr3:155587600-155590400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:155587600-155590400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:155587600-155590400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:155587600-155590400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:155587600-155590800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:155587600-155591000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:155587800-155590600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:155588000-155590400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:155588000-155590400	Active TSS	Fetal Stomach	stomach
13	chr3:155588000-155590400	Active TSS	Stomach Smooth Muscle	stomach
14	chr3:155588000-155590400	Active TSS	HSMMtube	muscle
15	chr3:155588000-155590400	Active TSS	NHDF-Ad	bronchial
16	chr3:155588000-155590600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:155588000-155590600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr3:155588000-155590600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:155588000-155590600	Active TSS	Brain Germinal Matrix	brain
20	chr3:155588000-155590800	Active TSS	NHLF	lung
21	chr3:155588000-155591000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr3:155588000-155591000	Active TSS	GM12878-XiMat	blood
23	chr3:155588000-155591800	Active TSS	K562	blood
24	chr3:155588200-155590800	Active TSS	HMEC	breast
25	chr3:155588600-155591000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr3:155589000-155590400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:155589200-155590400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr3:155589400-155590400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:155589400-155590600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:155589400-155591000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:155589600-155590400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr3:155589600-155590400	Flanking Active TSS	HUVEC	blood vessel
33	chr3:155589600-155590600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr3:155589600-155590600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:155589600-155590800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:155589600-155591000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:155589600-155599600	Weak transcription	Spleen	Spleen
38	chr3:155589800-155590400	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr3:155589800-155590400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr3:155589800-155590400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr3:155589800-155590400	Flanking Active TSS	Liver	Liver
42	chr3:155589800-155590400	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr3:155589800-155590400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:155589800-155590400	Flanking Active TSS	Fetal Lung	lung
45	chr3:155589800-155590400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr3:155589800-155590400	Flanking Active TSS	Hela-S3	cervix
47	chr3:155589800-155590400	Flanking Active TSS	NH-A	brain
48	chr3:155589800-155590400	Flanking Active TSS	Osteobl	bone
49	chr3:155589800-155590800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:155589800-155590800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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