Variant report

Variant	rs4743315
Chromosome Location	chr9:98538041-98538042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98536258..98539012-chr9:98551915..98554297,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs4743243	0.87[MEX][hapmap]
rs4743271	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4743272	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4743291	1.00[AFR][1000 genomes]
rs55878548	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62558997	1.00[AFR][1000 genomes]
rs62558998	1.00[AFR][1000 genomes]
rs62559000	0.83[AFR][1000 genomes]
rs62559001	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72756389	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72756391	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4743315	C9orf102	cis	parietal	SCAN
rs4743315	C9orf102	cis	cerebellum	SCAN
rs4743315	CTSL2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98534200-98539800	Weak transcription	Lung	lung
2	chr9:98534800-98539200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:98535200-98539000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:98535400-98538600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:98535400-98550800	Weak transcription	Right Atrium	heart
6	chr9:98535600-98538600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:98535600-98539800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:98535600-98545800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:98536000-98546800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:98536400-98541400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:98537000-98539000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:98537400-98541000	Weak transcription	HepG2	liver
13	chr9:98537600-98538600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:98537600-98539800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:98537800-98539000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:98537800-98539200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:98537800-98539200	Enhancers	Fetal Lung	lung
18	chr9:98537800-98539800	Enhancers	Fetal Stomach	stomach
19	chr9:98537800-98541200	Weak transcription	Ovary	ovary
20	chr9:98538000-98538400	Enhancers	Fetal Muscle Leg	muscle
21	chr9:98538000-98541800	Enhancers	NHLF	lung

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