Variant report

Variant	rs420436
Chromosome Location	chr6:28555998-28555999
allele	A/G
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	E2F4	chr6:28555966-28556148	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28456446..28459153-chr6:28555326..28557057,2	MCF-7	breast:

Variant related genes	Relation type
SCAND3	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10080420	0.81[ASN][1000 genomes]
rs10434846	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733177	1.00[ASN][1000 genomes]
rs10755647	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807032	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807036	0.83[ASN][1000 genomes]
rs10807040	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758055	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332986	0.81[ASN][1000 genomes]
rs1474986	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2057295	1.00[ASN][1000 genomes]
rs2108924	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2191036	0.81[ASN][1000 genomes]
rs2394119	1.00[ASN][1000 genomes]
rs28382606	1.00[ASN][1000 genomes]
rs2859375	1.00[JPT][hapmap]
rs34358978	0.93[ASN][1000 genomes]
rs34931542	0.93[ASN][1000 genomes]
rs3757180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs381493	1.00[ASN][1000 genomes]
rs384399	1.00[ASN][1000 genomes]
rs3852211	1.00[ASN][1000 genomes]
rs389603	1.00[ASN][1000 genomes]
rs392471	0.88[ASN][1000 genomes]
rs394772	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399558	0.97[ASN][1000 genomes]
rs3999023	1.00[ASN][1000 genomes]
rs402426	1.00[ASN][1000 genomes]
rs404343	1.00[ASN][1000 genomes]
rs408255	1.00[ASN][1000 genomes]
rs411538	1.00[ASN][1000 genomes]
rs4121090	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418628	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418898	1.00[ASN][1000 genomes]
rs420463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422089	0.97[ASN][1000 genomes]
rs424426	1.00[ASN][1000 genomes]
rs426922	1.00[ASN][1000 genomes]
rs429875	1.00[ASN][1000 genomes]
rs434636	1.00[ASN][1000 genomes]
rs442174	0.90[ASN][1000 genomes]
rs443924	1.00[ASN][1000 genomes]
rs449074	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454746	1.00[ASN][1000 genomes]
rs4711176	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713172	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713174	1.00[ASN][1000 genomes]
rs5007575	0.94[ASN][1000 genomes]
rs55860825	1.00[ASN][1000 genomes]
rs6456820	0.81[ASN][1000 genomes]
rs6456829	1.00[ASN][1000 genomes]
rs6456832	1.00[ASN][1000 genomes]
rs6456833	1.00[ASN][1000 genomes]
rs6899512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6906826	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912921	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6923163	1.00[ASN][1000 genomes]
rs6925972	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6935589	0.93[ASN][1000 genomes]
rs6937042	0.93[ASN][1000 genomes]
rs6941222	0.81[ASN][1000 genomes]
rs7381746	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7382159	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7382309	1.00[ASN][1000 genomes]
rs7382583	1.00[ASN][1000 genomes]
rs7761914	1.00[ASN][1000 genomes]
rs7771490	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773193	1.00[ASN][1000 genomes]
rs911177	1.00[ASN][1000 genomes]
rs911178	0.88[ASN][1000 genomes]
rs9393922	1.00[ASN][1000 genomes]
rs9393923	1.00[ASN][1000 genomes]
rs9461464	0.93[ASN][1000 genomes]
rs9468384	0.81[ASN][1000 genomes]
rs9468394	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28552400-28559600	Strong transcription	K562	blood
2	chr6:28553000-28558200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:28553200-28558200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28553200-28558600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:28553800-28556400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:28553800-28557600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:28553800-28558200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:28553800-28558400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:28553800-28558400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:28554000-28556000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28554000-28556000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr6:28554000-28556200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
13	chr6:28554000-28556200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:28554000-28558000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
15	chr6:28554200-28556000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr6:28554400-28556000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:28554400-28556000	Active TSS	A549	lung
18	chr6:28554400-28558400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:28554400-28558400	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr6:28554600-28556000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
21	chr6:28554600-28556200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:28554600-28557200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:28554800-28556000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:28555000-28556000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:28555200-28556200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
26	chr6:28555400-28556000	Flanking Active TSS	GM12878-XiMat	blood
27	chr6:28555400-28556200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
28	chr6:28555400-28556200	Flanking Active TSS	Hela-S3	cervix
29	chr6:28555400-28557200	Weak transcription	Spleen	Spleen
30	chr6:28555600-28556000	Flanking Active TSS	Fetal Brain Female	brain
31	chr6:28555600-28556000	Flanking Active TSS	HMEC	breast
32	chr6:28555600-28556200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:28555600-28556200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:28555600-28556200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:28555600-28557000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:28555600-28557200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:28555600-28557400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:28555800-28556000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:28555800-28556000	Bivalent Enhancer	Liver	Liver
40	chr6:28555800-28556000	Active TSS	Brain Germinal Matrix	brain
41	chr6:28555800-28556000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr6:28555800-28556000	Bivalent Enhancer	Pancreatic Islets	Pancreatic Islet
43	chr6:28555800-28556200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr6:28555800-28556200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:28555800-28556200	Bivalent Enhancer	Brain Hippocampus Middle	brain
46	chr6:28555800-28556200	Flanking Active TSS	NHEK	skin
47	chr6:28555800-28556400	Active TSS	HepG2	liver
48	chr6:28555800-28556600	Weak transcription	Fetal Brain Male	brain
49	chr6:28555800-28556600	Enhancers	Fetal Lung	lung
50	chr6:28555800-28556800	Bivalent Enhancer	Fetal Kidney	kidney

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