Variant report

Variant	rs9817530
Chromosome Location	chr3:24681883-24681884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24535344..24538472-chr3:24679344..24683508,5	MCF-7	breast:
2	chr3:24305875..24306747-chr3:24681516..24682374,2	K562	blood:
3	chr3:24400847..24401899-chr3:24681498..24682394,3	MCF-7	breast:
4	chr3:24681218..24682181-chr3:24725071..24725960,2	MCF-7	breast:
5	chr3:24305982..24306914-chr3:24681528..24682464,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11928551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17787397	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1865715	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2362754	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2362758	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4131483	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4328754	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4452272	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4544557	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4585138	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6550885	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6550887	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6762059	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6767967	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770162	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6771221	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6777417	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7613236	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7644196	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7652026	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9811110	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9812637	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9816563	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9843745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9848012	0.83[AMR][1000 genomes];0.89[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	esv2757862	chr3:24652513-24942926	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759135	chr3:24652513-24942926	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9817530	CMC1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24680400-24683400	Enhancers	Adipose Nuclei	Adipose
2	chr3:24680400-24683600	Enhancers	Fetal Intestine Small	intestine
3	chr3:24681000-24682400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:24681000-24683600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:24681000-24683800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:24681600-24682000	Enhancers	Brain Hippocampus Middle	brain
7	chr3:24681600-24682200	Enhancers	Fetal Lung	lung
8	chr3:24681600-24682400	Enhancers	NHDF-Ad	bronchial
9	chr3:24681600-24683800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:24681800-24682400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:24681800-24682800	Weak transcription	Fetal Intestine Large	intestine
12	chr3:24681800-24682800	Weak transcription	HUVEC	blood vessel
13	chr3:24681800-24683000	Weak transcription	Stomach Mucosa	stomach
14	chr3:24681800-24683800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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