Variant report

Variant	rs460165
Chromosome Location	chr3:161087710-161087711
allele	C/T
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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160956184..160959035-chr3:161087488..161089202,2	MCF-7	breast:
4	chr22:31475291..31477772-chr3:161087457..161089639,2	MCF-7	breast:
5	chr10:3825671..3828241-chr3:161086476..161088870,2	MCF-7	breast:
6	chr3:160999506..161001764-chr3:161085890..161088412,2	MCF-7	breast:
7	chr3:160787784..160789478-chr3:161085891..161088171,2	MCF-7	breast:
8	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
9	chr3:161087613..161089123-chr3:161278946..161281684,2	MCF-7	breast:
10	chr3:161086150..161088854-chr6:26156323..26158210,2	MCF-7	breast:
11	chr3:160502508..160504789-chr3:161086438..161088676,2	MCF-7	breast:
12	chr11:46622262..46624365-chr3:161085688..161088044,2	MCF-7	breast:
13	chr17:57181517..57184200-chr3:161086879..161089854,2	MCF-7	breast:
14	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:
15	chr3:160962510..160966697-chr3:161085167..161089151,3	MCF-7	breast:
16	chr3:161087384..161090083-chr9:131900097..131902606,2	MCF-7	breast:
17	chr20:45948103..45949754-chr3:161086879..161089062,2	MCF-7	breast:
18	chr3:63914213..63915723-chr3:161085984..161088284,2	MCF-7	breast:
19	chr16:89786488..89788334-chr3:161087418..161089454,2	MCF-7	breast:
20	chr15:99190324..99192171-chr3:161086732..161088826,2	MCF-7	breast:
21	chr16:83986674..83988846-chr3:161086778..161089338,2	MCF-7	breast:
22	chr2:199451456..199452956-chr3:161085880..161088129,3	MCF-7	breast:
23	chr12:12713891..12716367-chr3:161087265..161090021,2	MCF-7	breast:
24	chr14:19019125..19019628-chr3:161087703..161088203,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158805	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000119383	Chromatin interaction
ENSG00000075399	Chromatin interaction
ENSG00000140961	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000259424	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000067082	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10804790	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1154701	0.81[AMR][1000 genomes]
rs1382427	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1382428	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1478565	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1600209	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs163328	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs189270	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1993891	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2404340	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28515190	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs336541	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336543	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336548	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336549	0.81[EUR][1000 genomes]
rs336567	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336568	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs336569	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336570	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336572	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs336577	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336579	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336580	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs336582	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs336583	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336585	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336586	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336589	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336590	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336591	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336593	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs339101	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3849524	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4273380	0.83[EUR][1000 genomes]
rs4350933	0.85[EUR][1000 genomes]
rs4370045	0.82[EUR][1000 genomes]
rs4493448	0.84[EUR][1000 genomes]
rs455386	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs456611	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457272	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs459515	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs459697	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597724	0.85[EUR][1000 genomes]
rs460508	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461638	0.84[EUR][1000 genomes]
rs462413	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs462514	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs463928	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464766	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465985	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs466399	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279921	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6441370	0.81[AMR][1000 genomes]
rs6441371	0.81[AMR][1000 genomes]
rs6441373	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6762645	0.84[EUR][1000 genomes]
rs6765269	0.84[EUR][1000 genomes]
rs6775627	0.85[EUR][1000 genomes]
rs6794601	0.83[EUR][1000 genomes]
rs7611367	0.81[AMR][1000 genomes]
rs7615592	0.86[EUR][1000 genomes]
rs7623206	0.86[EUR][1000 genomes]
rs7629987	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7632797	0.81[AMR][1000 genomes]
rs7638668	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7647327	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7653233	0.87[EUR][1000 genomes]
rs7653361	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9290073	0.82[EUR][1000 genomes]
rs9290074	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs975323	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9790314	0.88[EUR][1000 genomes]
rs9821201	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9846756	0.85[EUR][1000 genomes]
rs9850455	0.88[EUR][1000 genomes]
rs9863590	0.83[EUR][1000 genomes]
rs9870059	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9872514	0.90[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv963570	chr3:161076656-161088849	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161084400-161088400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:161084400-161088800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:161084600-161088200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:161085400-161088200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:161085600-161088600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:161085800-161088400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:161086200-161088600	Weak transcription	Stomach Mucosa	stomach
9	chr3:161087200-161087800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:161087400-161087800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:161087600-161087800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:161087600-161088600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:161087600-161089200	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood

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