Variant report

Variant	rs6546026
Chromosome Location	chr2:63923699-63923700
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	FOS	chr2:63923635-63924077	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:63923634-63924127	MCF10A-Er-Src	breast:	n/a	chr2:63923957-63923980
3	FOS	chr2:63923696-63924090	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:63923652-63924072	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr2:63923675-63924653	MCF10A-Er-Src	breast:	n/a	chr2:63923957-63923980
6	STAT3	chr2:63923681-63924125	MCF10A-Er-Src	breast:	n/a	chr2:63923957-63923980
7	MYC	chr2:63923615-63924008	MCF10A-Er-Src	breast:	n/a	chr2:63923779-63923788 chr2:63923778-63923788 chr2:63923779-63923788 chr2:63923779-63923788 chr2:63923778-63923789 chr2:63923779-63923789

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63814867..63817469-chr2:63922056..63924960,2	MCF-7	breast:
2	chr2:63922943..63924879-chr2:64067283..64069747,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221085	TF binding region
ENSG00000014641	Chromatin interaction
ENSG00000169764	Chromatin interaction
ENSG00000143951	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10187013	0.95[CEU][hapmap];0.88[YRI][hapmap]
rs10201844	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10211360	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs10865343	0.85[CHB][hapmap]
rs11125985	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12612549	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs12612596	0.92[EUR][1000 genomes]
rs12613707	0.92[EUR][1000 genomes]
rs12713497	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs13006124	0.81[CHB][hapmap]
rs13384707	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17619717	0.81[CHB][hapmap]
rs2054119	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2592389	0.82[EUR][1000 genomes]
rs36042418	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4072113	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4359637	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4399712	0.90[EUR][1000 genomes]
rs4671526	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671528	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs4671532	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6546025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546027	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6546038	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs6546039	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs6737855	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6741298	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs6741584	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs6747307	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs9309356	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs998043	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834242	chr2:63891249-64045617	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63909200-63925600	Weak transcription	Psoas Muscle	Psoas
2	chr2:63919800-63925400	Weak transcription	A549	lung
3	chr2:63920800-63925800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:63921200-63925400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:63923000-63923800	Flanking Active TSS	Liver	Liver
6	chr2:63923000-63924200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:63923400-63923800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:63923400-63923800	Enhancers	Adipose Nuclei	Adipose
9	chr2:63923400-63924200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:63923400-63924200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:63923600-63923800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr2:63923600-63923800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:63923600-63923800	Enhancers	Osteobl	bone
14	chr2:63923600-63924000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:63923600-63924200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:63923600-63924200	Enhancers	NHEK	skin
17	chr2:63923600-63924400	Enhancers	HMEC	breast
18	chr2:63923600-63926000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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