Variant report

Variant	rs7000278
Chromosome Location	chr8:120215645-120215646
allele	G/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	chr8:120215364-120215941	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr8:120215275-120215828	SK-N-SH	brain:	n/a	n/a
3	CEBPB	chr8:120215375-120216075	Hela-S3	cervix:	n/a	n/a
4	BRCA1	chr8:120215374-120215992	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr8:120215306-120215790	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr8:120215371-120215991	MCF10A-Er-Src	breast:	n/a	n/a
7	RCOR1	chr8:120215407-120216018	Hela-S3	cervix:	n/a	n/a
8	RFX5	chr8:120215394-120216092	Hela-S3	cervix:	n/a	n/a
9	FOS	chr8:120215388-120215943	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:120203920..120207370-chr8:120214031..120217579,4	MCF-7	breast:
2	chr8:120211698..120216543-chr8:120218864..120221677,6	MCF-7	breast:
3	chr8:120210122..120216646-chr8:120218897..120222949,8	MCF-7	breast:

Variant related genes	Relation type
MAL2	TF binding region
ENSG00000147676	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10096921	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10113336	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13252588	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1364706	0.83[CHB][hapmap]
rs1364708	0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1385491	0.82[JPT][hapmap]
rs1425052	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425053	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1485291	0.82[JPT][hapmap]
rs1485292	0.82[JPT][hapmap]
rs1541726	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549415	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs17182246	0.85[CEU][hapmap];0.80[MEX][hapmap];0.83[EUR][1000 genomes]
rs1905774	0.82[JPT][hapmap]
rs2326222	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2450060	0.88[JPT][hapmap]
rs2450063	0.82[JPT][hapmap]
rs2450073	0.82[JPT][hapmap]
rs2450079	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs2465370	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2465373	0.89[ASN][1000 genomes]
rs2465377	0.89[ASN][1000 genomes]
rs2465379	0.89[ASN][1000 genomes]
rs2465389	0.82[JPT][hapmap]
rs2468171	0.80[CHB][hapmap]
rs2468173	0.84[ASN][1000 genomes]
rs2468184	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2468186	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4279627	0.82[JPT][hapmap]
rs4870897	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871362	0.83[CHB][hapmap]
rs6994957	0.83[CHB][hapmap]
rs7000127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7386676	0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs7825089	0.83[CHB][hapmap]
rs9656931	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7000278	NOV	cis	cerebellum	SCAN
rs7000278	MAL2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120212800-120218600	Weak transcription	Esophagus	oesophagus
2	chr8:120213400-120215800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:120213400-120215800	Weak transcription	Fetal Intestine Large	intestine
4	chr8:120213400-120215800	Enhancers	Hela-S3	cervix
5	chr8:120213800-120215800	Weak transcription	Adipose Nuclei	Adipose
6	chr8:120215000-120216000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:120215200-120217200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:120215200-120217600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr8:120215200-120219400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:120215200-120220000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr8:120215400-120216200	Enhancers	Liver	Liver
12	chr8:120215400-120217000	Enhancers	NHEK	skin
13	chr8:120215400-120219600	Enhancers	HMEC	breast
14	chr8:120215400-120219800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:120215600-120216200	Enhancers	Fetal Intestine Small	intestine
16	chr8:120215600-120216400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr8:120215600-120216400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:120215600-120217600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr8:120215600-120219400	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links