Variant report

Variant	rs62022573
Chromosome Location	chr15:50618291-50618292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50617729..50624931-chr15:50645125..50648613,9	MCF-7	breast:
2	chr15:50617564..50619195-chr15:50620939..50622477,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10152534	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10220734	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10220755	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11070766	0.85[EUR][1000 genomes]
rs11070768	0.86[EUR][1000 genomes]
rs11629603	0.86[EUR][1000 genomes]
rs11630045	0.85[EUR][1000 genomes]
rs11631985	0.85[EUR][1000 genomes]
rs11632703	0.86[EUR][1000 genomes]
rs11633903	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11636564	0.85[EUR][1000 genomes]
rs11637901	0.85[EUR][1000 genomes]
rs11638319	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11638432	0.85[EUR][1000 genomes]
rs11638564	0.85[EUR][1000 genomes]
rs11639406	0.85[EUR][1000 genomes]
rs11852487	0.86[EUR][1000 genomes]
rs11853236	0.86[EUR][1000 genomes]
rs11855823	0.86[EUR][1000 genomes]
rs12594956	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12901373	0.88[ASN][1000 genomes]
rs12902318	0.86[EUR][1000 genomes]
rs12910586	0.84[EUR][1000 genomes]
rs12912969	0.85[EUR][1000 genomes]
rs12913144	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1365504	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1645	0.85[EUR][1000 genomes]
rs16963604	0.85[EUR][1000 genomes]
rs16963612	0.87[EUR][1000 genomes]
rs17508371	0.85[EUR][1000 genomes]
rs1797311	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1972699	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2033115	0.86[EUR][1000 genomes]
rs2081628	0.85[EUR][1000 genomes]
rs2114447	0.89[ASN][1000 genomes]
rs28372114	0.86[EUR][1000 genomes]
rs28408662	0.80[EUR][1000 genomes]
rs28609286	0.86[EUR][1000 genomes]
rs28669213	0.86[EUR][1000 genomes]
rs28688566	0.85[EUR][1000 genomes]
rs28715646	0.85[EUR][1000 genomes]
rs28716586	0.85[EUR][1000 genomes]
rs28886692	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34197276	0.86[EUR][1000 genomes]
rs34590486	0.85[EUR][1000 genomes]
rs35000991	0.83[EUR][1000 genomes]
rs35024305	0.86[EUR][1000 genomes]
rs35168369	0.86[EUR][1000 genomes]
rs35777196	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3784297	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3985829	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4775874	0.85[EUR][1000 genomes]
rs4775875	0.85[EUR][1000 genomes]
rs4775876	0.86[EUR][1000 genomes]
rs4775877	0.86[EUR][1000 genomes]
rs489345	0.83[ASN][1000 genomes]
rs526045	0.85[EUR][1000 genomes]
rs535648	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493425	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493427	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493429	0.86[EUR][1000 genomes]
rs6493430	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7163457	0.86[EUR][1000 genomes]
rs7168233	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173127	0.83[EUR][1000 genomes]
rs7176792	0.85[EUR][1000 genomes]
rs8025367	0.84[EUR][1000 genomes]
rs8026571	0.85[EUR][1000 genomes]
rs8026785	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8027367	0.84[EUR][1000 genomes]
rs8030036	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8031431	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8034615	0.85[EUR][1000 genomes]
rs8036354	0.86[EUR][1000 genomes]
rs8039829	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8041259	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8042451	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8042845	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8043257	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs62022573	CTD-3110H11.1	cis	Thyroid	GTEx
rs62022573	GABPB1-AS1	cis	Artery Tibial	GTEx
rs62022573	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs62022573	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs62022573	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs62022573	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs62022573	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs62022573	GABPB1-AS1	cis	Artery Aorta	GTEx
rs62022573	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs62022573	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs62022573	CTD-3110H11.1	cis	lung	GTEx
rs62022573	GABPB1-AS1	cis	lung	GTEx
rs62022573	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs62022573	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs62022573	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs62022573	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50580800-50638400	Weak transcription	NHEK	skin
2	chr15:50596400-50623400	Weak transcription	Aorta	Aorta
3	chr15:50597000-50628600	Weak transcription	Fetal Stomach	stomach
4	chr15:50600800-50618600	Weak transcription	Fetal Intestine Large	intestine
5	chr15:50600800-50623200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:50600800-50629400	Weak transcription	Placenta	Placenta
7	chr15:50600800-50631200	Weak transcription	Left Ventricle	heart
8	chr15:50600800-50635400	Weak transcription	HepG2	liver
9	chr15:50600800-50641400	Weak transcription	HSMM	muscle
10	chr15:50600800-50641600	Weak transcription	Fetal Kidney	kidney
11	chr15:50600800-50643000	Weak transcription	Fetal Thymus	thymus
12	chr15:50600800-50643400	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:50600800-50644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:50600800-50644600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:50601000-50622800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:50601000-50627200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr15:50601000-50630400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr15:50601000-50637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:50601000-50638400	Weak transcription	HUVEC	blood vessel
20	chr15:50601400-50642800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:50602200-50621000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:50602200-50625600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:50608600-50623200	Weak transcription	A549	lung
24	chr15:50608800-50642800	Weak transcription	Hela-S3	cervix
25	chr15:50611200-50640400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:50611200-50641200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:50611400-50626800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:50611400-50641200	Weak transcription	Primary T cells from cord blood	blood
29	chr15:50611600-50626800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:50611600-50630600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:50611600-50640000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:50611800-50623200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:50611800-50630800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:50612400-50628400	Weak transcription	Fetal Intestine Small	intestine
35	chr15:50613400-50622800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:50613600-50622600	Weak transcription	Primary B cells from cord blood	blood
37	chr15:50613600-50633800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:50613800-50622600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:50613800-50623000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:50614400-50640800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:50615200-50644000	Weak transcription	HSMMtube	muscle
42	chr15:50615800-50640000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:50617800-50639200	Weak transcription	Ovary	ovary
44	chr15:50618200-50618400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:50618200-50629000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:50618200-50642400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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