Variant report

Variant	rs12651473
Chromosome Location	chr4:69772690-69772691
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	chr4:69213512..69216500-chr4:69770884..69773457,2	MCF-7	breast:
2	chr14:35451886..35454032-chr4:69771560..69773312,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UGT2A3-4	chr4:69772593-69772701	ENSG00000272626.1

Variant related genes	Relation type
ENSG00000083896	Chromatin interaction
ENSG00000100883	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11249509	0.80[ASN][1000 genomes]
rs11725828	0.82[ASN][1000 genomes]
rs11726946	0.88[EUR][1000 genomes]
rs11730594	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12647429	0.95[ASN][1000 genomes]
rs12649131	0.95[ASN][1000 genomes]
rs12649361	0.96[ASN][1000 genomes]
rs12650284	0.84[ASN][1000 genomes]
rs12650679	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12651295	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12651318	0.96[ASN][1000 genomes]
rs13129967	0.92[ASN][1000 genomes]
rs1458232	0.81[ASN][1000 genomes]
rs1458247	0.82[EUR][1000 genomes]
rs1598905	0.82[ASN][1000 genomes]
rs17146976	0.98[ASN][1000 genomes]
rs17147013	0.84[ASN][1000 genomes]
rs1841042	0.80[ASN][1000 genomes]
rs2670430	0.82[EUR][1000 genomes]
rs294772	0.80[ASN][1000 genomes]
rs4694367	0.80[ASN][1000 genomes]
rs4694390	0.82[ASN][1000 genomes]
rs58213278	0.95[ASN][1000 genomes]
rs59838953	0.95[ASN][1000 genomes]
rs6600856	0.82[ASN][1000 genomes]
rs6827243	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6835571	0.82[ASN][1000 genomes]
rs6851328	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6858469	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72849092	0.94[ASN][1000 genomes]
rs72849093	0.90[ASN][1000 genomes]
rs72849098	0.95[ASN][1000 genomes]
rs7665417	0.81[EUR][1000 genomes]
rs7668868	0.81[EUR][1000 genomes]
rs7678798	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7681837	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7682207	0.98[EUR][1000 genomes]
rs7691369	0.98[EUR][1000 genomes]
rs7693037	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9329036	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005513	chr4:69446718-69890307	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	esv3398036	chr4:69700493-69841391	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
6	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv436447	chr4:69743339-69851390	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv518690	chr4:69752468-69772694	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv4372	chr4:69764499-69810115	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69769400-69773400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:69769600-69773200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:69770000-69773000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr4:69770600-69772800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:69771400-69772800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr4:69771400-69773000	Active TSS	Duodenum Mucosa	Duodenum
7	chr4:69771600-69772800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:69771600-69772800	Active TSS	Liver	Liver
9	chr4:69771600-69772800	Active TSS	Hela-S3	cervix
10	chr4:69771600-69773200	Active TSS	Fetal Intestine Small	intestine
11	chr4:69771800-69772800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr4:69771800-69772800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:69771800-69773000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr4:69772000-69772800	Flanking Active TSS	Fetal Intestine Large	intestine
15	chr4:69772200-69772800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:69772200-69772800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:69772200-69773000	Active TSS	Fetal Stomach	stomach
18	chr4:69772200-69773000	Flanking Active TSS	Pancreas	Pancrea
19	chr4:69772200-69773200	Weak transcription	A549	lung
20	chr4:69772200-69774000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr4:69772400-69772800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr4:69772400-69772800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:69772400-69772800	Enhancers	Brain Hippocampus Middle	brain
24	chr4:69772400-69772800	Enhancers	Fetal Lung	lung
25	chr4:69772400-69772800	Enhancers	Fetal Muscle Trunk	muscle
26	chr4:69772400-69772800	Enhancers	Ovary	ovary
27	chr4:69772400-69772800	Enhancers	Right Atrium	heart
28	chr4:69772400-69772800	Enhancers	Stomach Mucosa	stomach
29	chr4:69772400-69773400	Enhancers	Fetal Kidney	kidney
30	chr4:69772400-69773600	Weak transcription	HepG2	liver
31	chr4:69772600-69772800	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr4:69772600-69772800	Enhancers	Esophagus	oesophagus
33	chr4:69772600-69773000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr4:69772600-69773200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:69772600-69773400	Enhancers	HUES48 Cell Line	embryonic stem cell

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