Variant report

Variant	rs62285462
Chromosome Location	chr3:99769834-99769835
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99768194..99771099-chr3:99774948..99777546,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10049383	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017968	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10212525	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021341	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10511177	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13064704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069311	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13093776	0.84[EUR][1000 genomes]
rs13093838	0.90[AMR][1000 genomes]
rs13323143	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1489816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17379739	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17392948	0.90[AMR][1000 genomes]
rs17393059	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291494	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28503408	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28714363	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28870092	0.82[AMR][1000 genomes]
rs34922392	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34996634	0.90[AMR][1000 genomes]
rs35154249	0.90[AMR][1000 genomes]
rs35521705	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35669453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35844878	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35885423	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4075038	0.81[EUR][1000 genomes]
rs4279135	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4571265	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928234	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285471	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285473	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285478	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790535	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790877	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799379	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802422	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806178	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6807176	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71313585	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610486	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7620228	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7627991	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs923470	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923471	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9814359	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815439	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823908	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828079	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9832186	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9833888	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9833980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834484	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837602	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9841186	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9851645	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852435	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853823	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9864437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873709	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873878	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875640	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875664	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878931	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62285462	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99752200-99774600	Weak transcription	Gastric	stomach
3	chr3:99762000-99778200	Weak transcription	Ovary	ovary
4	chr3:99765000-99772800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:99765800-99771800	Weak transcription	Hela-S3	cervix
6	chr3:99767000-99772000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:99767000-99772200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:99767000-99772400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:99767000-99772400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:99767000-99777000	Weak transcription	Aorta	Aorta
11	chr3:99767400-99772200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:99767400-99772200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:99767400-99772200	Weak transcription	Stomach Mucosa	stomach
14	chr3:99767400-99772400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:99767400-99773400	Weak transcription	Esophagus	oesophagus
16	chr3:99767400-99775000	Weak transcription	Psoas Muscle	Psoas
17	chr3:99767400-99779600	Weak transcription	Left Ventricle	heart
18	chr3:99767600-99772000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:99767600-99772000	Weak transcription	HSMMtube	muscle
20	chr3:99767600-99772200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:99767600-99772200	Weak transcription	HepG2	liver
22	chr3:99767600-99772400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:99767600-99772400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:99767600-99772800	Weak transcription	Adipose Nuclei	Adipose
25	chr3:99767600-99779400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:99767600-99801000	Weak transcription	HSMM	muscle
27	chr3:99767800-99774800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:99767800-99777000	Weak transcription	HMEC	breast
29	chr3:99768200-99780400	Weak transcription	GM12878-XiMat	blood
30	chr3:99768400-99788000	Weak transcription	Primary B cells from cord blood	blood
31	chr3:99768600-99771200	Weak transcription	Fetal Intestine Large	intestine
32	chr3:99769000-99771200	Weak transcription	Fetal Intestine Small	intestine
33	chr3:99769000-99776400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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