Variant report

Variant	rs28719542
Chromosome Location	chr8:48869511-48869512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:48868902-48870084	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:48869236..48871124-chr8:48909959..48911972,2	K562	blood:
2	chr8:48868410..48871024-chr8:48887533..48889835,2	MCF-7	breast:

Variant related genes	Relation type
MCM4	TF binding region
ENSG00000104738	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10093943	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10095249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10097429	0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11987748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11998483	0.94[AFR][1000 genomes]
rs17287711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28488251	1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28542480	0.98[AFR][1000 genomes]
rs28699569	0.88[AFR][1000 genomes]
rs28701667	0.89[AFR][1000 genomes]
rs28751111	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28812773	0.85[AFR][1000 genomes]
rs35590911	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6473874	0.85[AFR][1000 genomes]
rs6982203	0.89[AFR][1000 genomes]
rs6984595	0.88[AFR][1000 genomes]
rs7002719	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7819424	0.85[AFR][1000 genomes]
rs7828134	1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs7839604	0.85[AFR][1000 genomes]
rs7841307	1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8177999	0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8178024	0.94[AFR][1000 genomes]
rs8178037	0.94[AFR][1000 genomes]
rs8178117	0.85[AFR][1000 genomes]
rs8178176	0.83[AFR][1000 genomes]
rs8178185	0.85[AFR][1000 genomes]
rs8178240	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803608	chr8:48506628-48874811	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1021389	chr8:48700970-48880931	Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv539599	chr8:48700970-48880931	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv931032	chr8:48744329-49091359	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2758156	chr8:48788293-49008014	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv2759611	chr8:48788293-49008014	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv427820	chr8:48788293-49008014	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv831309	chr8:48815290-48977856	Strong transcription Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1033760	chr8:48852925-48961374	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48726400-48870400	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr8:48730000-48871600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:48739600-48870600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr8:48739800-48870400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr8:48793800-48870400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr8:48793800-48870800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr8:48820000-48871000	Strong transcription	Fetal Intestine Large	intestine
8	chr8:48820400-48870000	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr8:48820400-48870000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr8:48822400-48870800	Strong transcription	Liver	Liver
11	chr8:48822600-48870600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr8:48822600-48870800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr8:48823200-48870600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:48824200-48870200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr8:48824800-48870000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr8:48833800-48870800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:48833800-48870800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:48834400-48870200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr8:48835400-48870200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:48835800-48871600	Strong transcription	Primary B cells from cord blood	blood
21	chr8:48838800-48871000	Strong transcription	Primary T cells from cord blood	blood
22	chr8:48839200-48871400	Weak transcription	Right Atrium	heart
23	chr8:48839600-48869600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr8:48839600-48870600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr8:48839600-48871000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr8:48839800-48871200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr8:48846400-48871400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr8:48853400-48869600	Strong transcription	Fetal Brain Female	brain
29	chr8:48853600-48871000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:48855000-48871400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr8:48855400-48870600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr8:48855600-48871200	Strong transcription	Placenta	Placenta
33	chr8:48856200-48869600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr8:48857600-48871800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr8:48857800-48871800	Weak transcription	Stomach Mucosa	stomach
36	chr8:48858000-48871000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:48858200-48869600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr8:48858200-48869800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr8:48858200-48871000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr8:48859000-48870000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr8:48859400-48871400	Strong transcription	Fetal Thymus	thymus
42	chr8:48861200-48870400	Strong transcription	NH-A	brain
43	chr8:48861200-48870600	Strong transcription	A549	lung
44	chr8:48861400-48869800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr8:48861400-48870000	Strong transcription	Osteobl	bone
46	chr8:48861400-48870400	Strong transcription	K562	blood
47	chr8:48861400-48870600	Strong transcription	Hela-S3	cervix
48	chr8:48861600-48870800	Strong transcription	HepG2	liver
49	chr8:48861600-48871200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr8:48861600-48871200	Strong transcription	HSMM	muscle

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