Variant report

Variant	rs10761348
Chromosome Location	chr9:97405262-97405263
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:58637930..58639560-chr9:97403785..97405324,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267678	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10114605	0.84[EUR][1000 genomes]
rs10123016	0.93[EUR][1000 genomes]
rs10123666	0.91[EUR][1000 genomes]
rs10761345	0.84[EUR][1000 genomes]
rs10761347	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10993267	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs10993271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993276	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1410972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402381	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3739747	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs3780554	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs3780555	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4129220	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4744360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744363	0.81[ASN][1000 genomes]
rs6479561	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7025121	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7031924	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041301	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7041595	0.83[AMR][1000 genomes];0.97[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	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10761348	CENPP	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97402200-97410400	Weak transcription	Esophagus	oesophagus
2	chr9:97402400-97406600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr9:97402400-97420000	Weak transcription	Right Atrium	heart
4	chr9:97402600-97411000	Weak transcription	Gastric	stomach
5	chr9:97402600-97415400	Weak transcription	Spleen	Spleen
6	chr9:97402800-97405600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:97402800-97411600	Weak transcription	Primary B cells from cord blood	blood
8	chr9:97403000-97406800	Weak transcription	Fetal Intestine Large	intestine
9	chr9:97403000-97406800	Weak transcription	Placenta	Placenta
10	chr9:97403000-97410600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:97403200-97405600	Weak transcription	Stomach Mucosa	stomach
12	chr9:97403200-97406600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:97403400-97406800	Weak transcription	Fetal Intestine Small	intestine
14	chr9:97404000-97408200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:97404800-97405400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr9:97404800-97405600	Enhancers	Lung	lung
17	chr9:97404800-97406200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:97405000-97406400	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr9:97405000-97410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:97405200-97411200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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