Variant report

Variant	rs1557698
Chromosome Location	chr7:112050437-112050438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr7:112050341-112050528	MCF10A-Er-Src	breast:	n/a	chr7:112050494-112050501
2	JUND	chr7:112050260-112050629	Hela-S3	cervix:	n/a	n/a
3	FOS	chr7:112050222-112050612	MCF10A-Er-Src	breast:	n/a	n/a
4	JUND	chr7:112049554-112051862	SK-N-SH	brain:	n/a	n/a
5	SMC3	chr7:112050105-112051862	SK-N-SH	brain:	n/a	chr7:112050653-112050661
6	RAD21	chr7:112050034-112052306	SK-N-SH	brain:	n/a	n/a
7	FOS	chr7:112050210-112050622	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr7:112050243-112050611	MCF10A-Er-Src	breast:	n/a	n/a
9	FOSL2	chr7:112050115-112050695	SK-N-SH	brain:	n/a	n/a
10	FOS	chr7:112050196-112050615	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:112049730..112052171-chr7:112053926..112056276,3	K562	blood:
2	chr7:112045125..112048422-chr7:112049738..112053855,5	K562	blood:
3	chr7:111494801..111495981-chr7:112050100..112051106,3	MCF-7	breast:
4	chr7:112048671..112054554-chr7:112088966..112092653,8	K562	blood:
5	chr7:112049693..112052446-chr7:112089375..112092902,3	K562	blood:
6	chr7:111592856..111595719-chr7:112049563..112051825,3	MCF-7	breast:
7	chr7:112045125..112047686-chr7:112049738..112051786,2	K562	blood:
8	chr7:112047884..112050486-chr7:112089235..112093334,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226851	TF binding region
ENSG00000222346	Chromatin interaction
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1015417	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17492150	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2396537	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2520468	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2520469	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2520472	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2520478	0.85[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2520479	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2520480	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2520481	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2520483	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2520484	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523036	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523043	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708591	0.89[ASN][1000 genomes]
rs2708593	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708599	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708600	0.80[MEX][hapmap]
rs36113101	0.84[ASN][1000 genomes]
rs6977129	0.82[ASN][1000 genomes]
rs727807	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs728273	0.83[CEU][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789649	0.80[MEX][hapmap]
rs9640740	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs991632	0.99[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	nsv532335	chr7:111411990-112054905	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
3	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1557698	C7orf53	cis	cerebellum	SCAN
rs1557698	PPP1R1A	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112046000-112050600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:112046000-112050800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:112046000-112051000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:112046000-112060400	Weak transcription	Brain Angular Gyrus	brain
5	chr7:112048400-112050600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:112049600-112051200	Enhancers	Fetal Lung	lung
7	chr7:112050000-112050600	Enhancers	Placenta Amnion	Placenta Amnion
8	chr7:112050000-112051400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:112050200-112051800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:112050400-112050800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:112050400-112051400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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