Variant report

Variant	rs56046902
Chromosome Location	chr14:39884876-39884877
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39882950..39886541-chr14:39887581..39892204,4	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11157067	0.86[AFR][1000 genomes]
rs11847057	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12232110	0.94[ASN][1000 genomes]
rs12587625	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12588110	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12588175	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12588483	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12589427	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12590172	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12880644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12882250	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12883652	0.84[ASN][1000 genomes]
rs12884747	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12886769	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12894855	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12897960	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17109300	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17109328	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1950329	0.95[AFR][1000 genomes]
rs1950334	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1950336	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1950338	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1955718	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2038278	0.84[ASN][1000 genomes]
rs2057137	0.80[AMR][1000 genomes]
rs2057138	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2104531	0.81[ASN][1000 genomes]
rs2207291	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274395	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2415549	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2415550	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899888	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2899889	0.91[ASN][1000 genomes]
rs34432449	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34649642	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34687394	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs34928332	0.81[ASN][1000 genomes]
rs35115885	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35459433	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35553183	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35643160	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs35693868	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35876588	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35923045	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs36010374	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3814860	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4899245	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4899277	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4899278	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4899291	0.94[AFR][1000 genomes]
rs4902569	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4902570	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4902598	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902599	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902622	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902636	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902637	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902648	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902665	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902676	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902692	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs67439322	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs67963654	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs71407788	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71407789	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7140983	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7145821	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7148377	0.84[ASN][1000 genomes]
rs7152341	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7152935	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7153413	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7158709	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7161403	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs718364	0.84[ASN][1000 genomes]
rs72675487	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8003397	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8003621	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8006123	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8006321	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8020250	0.94[AFR][1000 genomes]
rs910370	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910371	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9332387	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39862000-39886000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:39863400-39891600	Weak transcription	Small Intestine	intestine
3	chr14:39864600-39898800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr14:39865000-39891200	Weak transcription	Psoas Muscle	Psoas
5	chr14:39865000-39898200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:39869000-39886200	Weak transcription	Aorta	Aorta
7	chr14:39869000-39886200	Weak transcription	Ovary	ovary
8	chr14:39869000-39895600	Weak transcription	Hela-S3	cervix
9	chr14:39870400-39885200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:39871000-39886200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr14:39871200-39885200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr14:39872400-39885200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr14:39881200-39886800	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr14:39881200-39887200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:39881600-39887200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr14:39882200-39895400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:39882600-39885200	Weak transcription	Fetal Heart	heart
18	chr14:39884000-39886200	Weak transcription	Left Ventricle	heart
19	chr14:39884600-39886000	Weak transcription	Thymus	Thymus
20	chr14:39884800-39885600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr14:39884800-39886600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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