Variant report

Variant	rs28428559
Chromosome Location	chr3:50473164-50473165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50473157..50474126-chr3:50579445..50580285,9	MCF-7	breast:
2	chr3:50374572..50376735-chr3:50471346..50473701,3	K562	blood:
3	chr3:50456429..50459348-chr3:50470888..50473813,2	MCF-7	breast:
4	chr3:50471606..50474364-chr3:50476758..50479663,3	K562	blood:
5	chr3:50386862..50388722-chr3:50472468..50474330,2	MCF-7	breast:
6	chr3:50472878..50473722-chr3:50651256..50652161,4	K562	blood:

Variant related genes	Relation type
ENSG00000202322	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000272104	Chromatin interaction
ENSG00000114388	Chromatin interaction
ENSG00000114395	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1034408	1.00[EUR][1000 genomes]
rs1034409	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157328	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2187815	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236966	1.00[ASN][1000 genomes]
rs2236969	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236970	1.00[ASN][1000 genomes]
rs2236972	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236976	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236977	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236978	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236980	0.94[ASN][1000 genomes]
rs2236982	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236985	0.97[ASN][1000 genomes]
rs2236990	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282757	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282761	0.94[ASN][1000 genomes]
rs28493735	0.91[ASN][1000 genomes]
rs28580410	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28593422	1.00[EUR][1000 genomes]
rs3213520	1.00[ASN][1000 genomes]
rs4422301	1.00[EUR][1000 genomes]
rs55790255	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55876418	1.00[EUR][1000 genomes]
rs55892059	1.00[EUR][1000 genomes]
rs56114301	1.00[EUR][1000 genomes]
rs56249615	1.00[EUR][1000 genomes]
rs56258146	1.00[EUR][1000 genomes]
rs56766970	1.00[EUR][1000 genomes]
rs57405128	1.00[EUR][1000 genomes]
rs57415469	1.00[EUR][1000 genomes]
rs58412961	1.00[EUR][1000 genomes]
rs58462551	0.91[ASN][1000 genomes]
rs59012751	1.00[EUR][1000 genomes]
rs59167171	0.91[ASN][1000 genomes]
rs59619552	1.00[ASN][1000 genomes]
rs59790001	1.00[EUR][1000 genomes]
rs60149721	1.00[EUR][1000 genomes]
rs60273100	0.90[EUR][1000 genomes]
rs60391761	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60697422	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61413553	1.00[EUR][1000 genomes]
rs61493458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767505	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770258	1.00[EUR][1000 genomes]
rs6770669	1.00[EUR][1000 genomes]
rs73832879	1.00[EUR][1000 genomes]
rs73832881	1.00[EUR][1000 genomes]
rs73833363	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73833366	1.00[EUR][1000 genomes]
rs73833371	1.00[EUR][1000 genomes]
rs73833372	0.82[EUR][1000 genomes]
rs73833373	1.00[EUR][1000 genomes]
rs73833386	1.00[EUR][1000 genomes]
rs73835503	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73835505	1.00[EUR][1000 genomes]
rs743754	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743755	1.00[EUR][1000 genomes]
rs7610830	1.00[EUR][1000 genomes]
rs7612820	1.00[EUR][1000 genomes]
rs7625295	1.00[EUR][1000 genomes]
rs7626470	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634307	1.00[EUR][1000 genomes]
rs7640842	1.00[EUR][1000 genomes]
rs7642779	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7647409	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649603	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311451	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9311453	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9311455	0.97[ASN][1000 genomes]
rs9812540	0.94[ASN][1000 genomes]
rs9814606	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9817768	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9828829	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832993	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9834579	0.91[ASN][1000 genomes]
rs9834856	0.91[ASN][1000 genomes]
rs9837658	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837861	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9839266	0.91[ASN][1000 genomes]
rs9839996	1.00[ASN][1000 genomes]
rs9843693	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9854585	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863307	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9863857	0.97[ASN][1000 genomes]
rs9875233	1.00[ASN][1000 genomes]
rs9880285	0.94[ASN][1000 genomes]
rs9883635	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9990256	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
8	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
10	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
11	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
12	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
15	esv3445182	chr3:50458687-50496660	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50465600-50485800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:50465800-50487000	Weak transcription	Fetal Intestine Small	intestine
3	chr3:50468200-50473400	Weak transcription	Right Ventricle	heart
4	chr3:50468200-50474600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:50468800-50478800	Weak transcription	Fetal Lung	lung
6	chr3:50468800-50480200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:50469000-50473200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:50469000-50475800	Weak transcription	Brain Anterior Caudate	brain
9	chr3:50469200-50473200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:50469200-50473400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:50469800-50473400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:50470200-50479000	Weak transcription	Left Ventricle	heart
13	chr3:50470400-50473200	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:50471200-50479800	Enhancers	Fetal Heart	heart
15	chr3:50471400-50474200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr3:50471600-50479600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:50471800-50474000	Enhancers	Fetal Thymus	thymus
18	chr3:50471800-50475200	Weak transcription	Spleen	Spleen
19	chr3:50471800-50477800	Weak transcription	Gastric	stomach
20	chr3:50472000-50474400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr3:50472000-50475400	Weak transcription	Lung	lung
22	chr3:50472200-50473800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:50472200-50473800	Weak transcription	Right Atrium	heart
24	chr3:50472200-50477000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:50472400-50473800	Bivalent Enhancer	Fetal Brain Male	brain
26	chr3:50472400-50474000	Enhancers	Brain Germinal Matrix	brain
27	chr3:50472600-50473400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:50472600-50473600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:50472600-50473600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:50472600-50474000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:50472800-50473800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:50472800-50474000	Enhancers	K562	blood
33	chr3:50473000-50473400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:50473000-50473600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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