Variant report

Variant	rs418628
Chromosome Location	chr6:28553499-28553500
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	STAT3	chr6:28553099-28553529	MCF10A-Er-Src	breast:	n/a	chr6:28553285-28553296
2	FOS	chr6:28553208-28553526	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr6:28553163-28553592	MCF10A-Er-Src	breast:	n/a	chr6:28553285-28553296
4	MYC	chr6:28553176-28553521	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr6:28553076-28553505	MCF10A-Er-Src	breast:	n/a	chr6:28553285-28553296
6	FOS	chr6:28553145-28553520	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr6:28553303-28553502	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr6:28552877-28553529	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr6:28553000-28553512	MCF10A-Er-Src	breast:	n/a	chr6:28553285-28553296
10	STAT3	chr6:28553075-28553505	MCF10A-Er-Src	breast:	n/a	chr6:28553285-28553296
11	FOS	chr6:28553126-28553529	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28551064..28553873-chr7:151215721..151217781,2	MCF-7	breast:
2	chr6:28548777..28553647-chr6:28554633..28557663,4	K562	blood:

Variant related genes	Relation type
ENSG00000246350	TF binding region
ENSG00000232040	Chromatin interaction
ENSG00000246350	Chromatin interaction
ENSG00000106615	Chromatin interaction

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	0.92[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	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807032	0.92[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	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758055	0.92[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	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2057295	1.00[ASN][1000 genomes]
rs2108924	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	0.86[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]
rs418898	1.00[ASN][1000 genomes]
rs420436	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420463	0.94[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	0.89[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	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713172	0.91[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	0.88[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	0.92[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[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	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7382159	0.92[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	0.91[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	0.92[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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28535000-28554000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:28537200-28554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:28537400-28553800	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:28540000-28554000	Weak transcription	Gastric	stomach
5	chr6:28540600-28554200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:28541000-28554200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:28541400-28554000	Weak transcription	Pancreas	Pancrea
8	chr6:28548000-28554000	Weak transcription	Right Atrium	heart
9	chr6:28548200-28554000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:28550600-28554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:28551000-28554000	Weak transcription	Right Ventricle	heart
12	chr6:28551600-28554000	Enhancers	Fetal Lung	lung
13	chr6:28552200-28554000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:28552200-28554600	Flanking Active TSS	Fetal Brain Female	brain
15	chr6:28552400-28553600	Enhancers	HepG2	liver
16	chr6:28552400-28559600	Strong transcription	K562	blood
17	chr6:28552800-28553600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:28552800-28553800	Enhancers	Fetal Intestine Large	intestine
19	chr6:28553000-28553600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:28553000-28553600	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr6:28553000-28553600	Enhancers	HMEC	breast
22	chr6:28553000-28553800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:28553000-28554000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr6:28553000-28554000	Enhancers	Fetal Intestine Small	intestine
25	chr6:28553000-28554000	Enhancers	GM12878-XiMat	blood
26	chr6:28553000-28554000	Enhancers	NHEK	skin
27	chr6:28553000-28554400	Enhancers	NH-A	brain
28	chr6:28553000-28558200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:28553200-28553600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:28553200-28553800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:28553200-28554000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:28553200-28554000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:28553200-28554000	Enhancers	Liver	Liver
34	chr6:28553200-28554000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:28553200-28554200	Enhancers	Fetal Heart	heart
36	chr6:28553200-28554400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:28553200-28558200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr6:28553200-28558600	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:28553400-28553600	Flanking Active TSS	Fetal Brain Male	brain
40	chr6:28553400-28553800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr6:28553400-28554000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:28553400-28554000	Weak transcription	Fetal Kidney	kidney
43	chr6:28553400-28554000	Enhancers	Hela-S3	cervix

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