Variant report

Variant	rs4774857
Chromosome Location	chr15:56717366-56717367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56714747..56716284-chr15:56716589..56718483,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10152826	0.81[EUR][1000 genomes]
rs10438327	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1072358	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852414	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11853962	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854726	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11855937	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11856170	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11856691	0.92[EUR][1000 genomes]
rs11857306	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11857374	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858489	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12324006	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12708449	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898789	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12901182	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902594	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907445	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12908839	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12910210	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12910212	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13379498	0.82[ASN][1000 genomes]
rs1402171	0.84[EUR][1000 genomes]
rs1426069	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1426070	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1477588	0.85[EUR][1000 genomes]
rs1520532	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17238691	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17819444	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1863425	0.85[EUR][1000 genomes]
rs1991266	0.85[EUR][1000 genomes]
rs2098897	0.85[EUR][1000 genomes]
rs2114185	0.85[EUR][1000 genomes]
rs2465968	0.85[EUR][1000 genomes]
rs2554284	0.84[EUR][1000 genomes]
rs2554287	0.85[EUR][1000 genomes]
rs2554288	0.85[EUR][1000 genomes]
rs2682013	0.85[EUR][1000 genomes]
rs2682016	0.83[EUR][1000 genomes]
rs2682024	0.85[EUR][1000 genomes]
rs2682025	0.85[EUR][1000 genomes]
rs2682026	0.85[EUR][1000 genomes]
rs2682027	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2713919	0.85[EUR][1000 genomes]
rs2713921	0.85[EUR][1000 genomes]
rs2713940	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718904	0.85[EUR][1000 genomes]
rs2718905	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718921	0.84[EUR][1000 genomes]
rs2718922	0.84[EUR][1000 genomes]
rs2718923	0.85[EUR][1000 genomes]
rs2718947	0.84[EUR][1000 genomes]
rs2725850	0.84[EUR][1000 genomes]
rs2725851	0.84[EUR][1000 genomes]
rs2725852	0.84[EUR][1000 genomes]
rs2725853	0.84[EUR][1000 genomes]
rs2725855	0.84[EUR][1000 genomes]
rs2725856	0.84[EUR][1000 genomes]
rs2725857	0.85[EUR][1000 genomes]
rs2725861	0.85[EUR][1000 genomes]
rs28622888	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28866008	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34544252	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34597546	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34684027	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35131119	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35155290	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35187662	0.80[EUR][1000 genomes]
rs35361016	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35470681	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35570374	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35895864	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35968448	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36082281	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784551	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774238	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4774239	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774852	0.91[EUR][1000 genomes]
rs4774854	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4774855	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4774860	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56319062	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57947969	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60328780	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60648061	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61010710	0.92[EUR][1000 genomes]
rs61288444	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62022130	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62023869	0.89[EUR][1000 genomes]
rs62047375	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62047376	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62047377	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6493844	0.86[EUR][1000 genomes]
rs67347418	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67639563	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs724100	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs767142	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8032826	0.86[EUR][1000 genomes]
rs8041422	0.82[EUR][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	nsv1545	chr15:56659498-56897381	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS 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	4 gene(s)	inside rSNPs	diseases
2	nsv1046891	chr15:56659587-56792033	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv471330	chr15:56659709-56896385	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471506	chr15:56659709-56896385	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv904246	chr15:56665827-56732192	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv498847	chr15:56667038-56896395	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2525559	chr15:56669294-56897412	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv433294	chr15:56676457-56853535	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3693203	chr15:56676457-56894478	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv35150	chr15:56677730-56896304	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510662	chr15:56686353-56735547	Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv9270	chr15:56686946-56760420	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56665200-56733400	Weak transcription	Fetal Kidney	kidney
2	chr15:56677800-56726200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:56686000-56734600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:56690000-56717400	Weak transcription	Dnd41	blood
5	chr15:56690000-56737800	Weak transcription	Stomach Mucosa	stomach
6	chr15:56699200-56717800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:56703600-56718000	Weak transcription	Fetal Intestine Large	intestine
8	chr15:56703600-56730800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:56704000-56734600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:56704800-56717800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:56705400-56734800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:56707200-56718000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:56711600-56724000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:56713400-56718000	Weak transcription	HSMMtube	muscle
15	chr15:56715400-56718200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:56715400-56723000	Weak transcription	Fetal Stomach	stomach
17	chr15:56716000-56718000	Weak transcription	Thymus	Thymus
18	chr15:56716000-56718600	ZNF genes & repeats	GM12878-XiMat	blood
19	chr15:56716000-56756600	Weak transcription	HSMM	muscle
20	chr15:56716200-56717800	Weak transcription	Fetal Thymus	thymus
21	chr15:56716200-56718000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:56716400-56718000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:56716600-56718800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:56716600-56725600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:56716800-56734600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:56717200-56718200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr15:56717200-56718200	ZNF genes & repeats	Fetal Brain Female	brain
28	chr15:56717200-56718600	ZNF genes & repeats	Fetal Lung	lung
29	chr15:56717200-56719600	Weak transcription	Brain Angular Gyrus	brain

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