Variant report

Variant	rs62241295
Chromosome Location	chr3:20010307-20010308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20008792..20011141-chr3:20013456..20016159,2	MCF-7	breast:
2	chr3:20007536..20010825-chr3:20014102..20016831,3	K562	blood:
3	chr3:20007751..20010574-chr3:20010896..20013275,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510497	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374092	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486526	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488378	1.00[ASN][1000 genomes]
rs12490848	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495866	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497549	1.00[ASN][1000 genomes]
rs17181337	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365374	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28597881	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241539	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398451	1.00[ASN][1000 genomes]
rs45542931	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618239	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858116	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858632	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858664	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858674	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797296	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55892327	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241279	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241280	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241286	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62241289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241316	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241322	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241326	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241330	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241333	1.00[ASN][1000 genomes]
rs62241334	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241337	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62243065	1.00[ASN][1000 genomes]
rs62243074	1.00[ASN][1000 genomes]
rs62243075	1.00[ASN][1000 genomes]
rs62243076	1.00[ASN][1000 genomes]
rs73032477	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034166	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
4	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
6	chr3:19993600-20015600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:19993600-20023600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:19993800-20016200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:19993800-20023800	Weak transcription	Small Intestine	intestine
10	chr3:19994000-20015800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:19994000-20017400	Weak transcription	HSMMtube	muscle
12	chr3:19994600-20011600	Weak transcription	Brain Substantia Nigra	brain
13	chr3:19994600-20013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:19995600-20017000	Weak transcription	Brain Germinal Matrix	brain
15	chr3:19995800-20016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:19995800-20021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:19996400-20017200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:19996400-20021000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:19996600-20015600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:19996600-20016800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:19997200-20013200	Weak transcription	HMEC	breast
22	chr3:19997200-20017000	Weak transcription	HUVEC	blood vessel
23	chr3:19997600-20011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:19997600-20015200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:19997800-20013200	Weak transcription	NHLF	lung
26	chr3:19997800-20015400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:19997800-20015600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:19997800-20016200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:19997800-20017000	Weak transcription	Brain Anterior Caudate	brain
30	chr3:19997800-20023200	Weak transcription	Spleen	Spleen
31	chr3:19998000-20011800	Weak transcription	Gastric	stomach
32	chr3:19998000-20017000	Weak transcription	HepG2	liver
33	chr3:19998200-20013200	Weak transcription	Osteobl	bone
34	chr3:19998400-20013200	Weak transcription	NHDF-Ad	bronchial
35	chr3:19998800-20011800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:19998800-20013600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:19999000-20011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:19999000-20013400	Weak transcription	NH-A	brain
39	chr3:19999200-20011800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:19999600-20027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:20000400-20011800	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:20000600-20011800	Weak transcription	GM12878-XiMat	blood
43	chr3:20000800-20015600	Weak transcription	Fetal Lung	lung
44	chr3:20002000-20011600	Weak transcription	Ovary	ovary
45	chr3:20002200-20015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:20002400-20013200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:20002600-20011800	Weak transcription	Brain Angular Gyrus	brain
48	chr3:20003600-20011600	Weak transcription	Fetal Thymus	thymus
49	chr3:20003800-20011600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:20003800-20013000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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