Variant report

Variant	rs73220932
Chromosome Location	chr3:139253489-139253490
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139252110..139254375-chr3:139256957..139258581,2	MCF-7	breast:
2	chr3:139253381..139256319-chr3:139269568..139271702,2	MCF-7	breast:
3	chr3:139251954..139254660-chr3:139259598..139262357,2	MCF-7	breast:
4	chr3:139251496..139253555-chr3:139254279..139256942,2	MCF-7	breast:
5	chr3:139252531..139254445-chr3:139267067..139268675,2	MCF-7	breast:
6	chr3:139239944..139241919-chr3:139253042..139255747,2	MCF-7	breast:
7	chr3:139245782..139250222-chr3:139250781..139254846,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114115	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1116748	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11549984	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489687	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493507	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391029	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391030	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391031	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511570	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511571	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17337746	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397112	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011770	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772868	0.93[EUR][1000 genomes]
rs3821543	0.93[EUR][1000 genomes]
rs4270469	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407373	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683502	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55641400	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55642746	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724241	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780517	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55817881	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55834130	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55968289	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987999	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034427	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051054	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051514	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058641	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56170893	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56210757	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343214	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs57459746	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220940	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220941	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220944	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220945	0.97[ASN][1000 genomes]
rs893703	0.93[EUR][1000 genomes]
rs930412	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139235000-139253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:139249600-139254400	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:139249600-139255000	Enhancers	Pancreas	Pancrea
4	chr3:139249600-139256400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:139249800-139253800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:139249800-139257400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:139250000-139256600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:139250200-139255000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:139250200-139255000	Enhancers	Brain Anterior Caudate	brain
10	chr3:139250600-139254600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:139250600-139254600	Enhancers	Fetal Lung	lung
12	chr3:139250600-139255400	Enhancers	Brain Angular Gyrus	brain
13	chr3:139250600-139256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:139250800-139254400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:139250800-139257400	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:139251000-139254600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:139251000-139255800	Enhancers	Fetal Kidney	kidney
18	chr3:139251200-139254200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:139251200-139254400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:139251200-139254600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:139251200-139254600	Enhancers	Fetal Intestine Large	intestine
22	chr3:139251200-139255800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:139251200-139257400	Genic enhancers	Fetal Intestine Small	intestine
24	chr3:139251400-139254200	Enhancers	HepG2	liver
25	chr3:139251400-139255400	Enhancers	Placenta	Placenta
26	chr3:139251400-139256400	Enhancers	Liver	Liver
27	chr3:139251400-139257200	Enhancers	Duodenum Mucosa	Duodenum
28	chr3:139251600-139254600	Enhancers	Fetal Muscle Leg	muscle
29	chr3:139251600-139255800	Enhancers	Fetal Brain Male	brain
30	chr3:139251600-139256400	Enhancers	HMEC	breast
31	chr3:139251800-139254400	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr3:139251800-139254600	Enhancers	Fetal Muscle Trunk	muscle
33	chr3:139251800-139255200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:139251800-139258600	Enhancers	Fetal Heart	heart
35	chr3:139252000-139253600	Enhancers	Stomach Smooth Muscle	stomach
36	chr3:139252000-139254600	Flanking Active TSS	NH-A	brain
37	chr3:139252000-139254800	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr3:139252000-139254800	Enhancers	Fetal Brain Female	brain
39	chr3:139252000-139257600	Enhancers	Left Ventricle	heart
40	chr3:139252200-139257600	Enhancers	Brain Substantia Nigra	brain
41	chr3:139252400-139254800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:139252400-139256200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:139252600-139253800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:139252600-139254200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:139252600-139254200	Flanking Active TSS	Hela-S3	cervix
46	chr3:139252600-139254400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr3:139252600-139254400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:139252600-139254400	Enhancers	Muscle Satellite Cultured Cells	--
49	chr3:139252600-139254800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:139252600-139254800	Enhancers	Esophagus	oesophagus

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