Variant report

Variant	rs10169185
Chromosome Location	chr2:55658836-55658837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55466615..55468826-chr2:55656150..55659154,3	MCF-7	breast:
2	chr2:55644901..55646531-chr2:55657733..55659340,2	MCF-7	breast:
3	chr2:55652880..55655236-chr2:55657266..55660173,3	MCF-7	breast:
4	chr2:55645665..55649753-chr2:55657366..55660139,6	K562	blood:
5	chr2:55651546..55653549-chr2:55657687..55659327,2	K562	blood:
6	chr2:55462241..55464416-chr2:55656583..55659722,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11125568	0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11125569	0.84[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11125572	0.86[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11695152	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12617891	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs12618795	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1454415	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1454419	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1545554	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs1598163	1.00[CEU][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1902057	0.89[GIH][hapmap];0.82[MEX][hapmap]
rs1902061	0.85[CEU][hapmap]
rs1902062	0.89[AMR][1000 genomes]
rs2045135	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2100454	0.90[ASN][1000 genomes]
rs2123983	0.89[GIH][hapmap];0.82[MEX][hapmap]
rs28501559	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2867194	0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs3099080	0.82[MEX][hapmap]
rs4233961	0.83[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4277563	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4352263	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4672032	0.86[ASN][1000 genomes]
rs4672033	0.87[ASN][1000 genomes]
rs4672034	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4672035	0.83[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4672040	0.94[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4672043	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4672044	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4672045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56225989	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545489	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6545490	0.84[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs6545492	0.81[EUR][1000 genomes]
rs6709204	0.82[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6720698	0.81[EUR][1000 genomes]
rs6724840	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6733814	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7559987	0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7574743	0.80[AMR][1000 genomes]
rs7579037	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7586440	0.86[JPT][hapmap]
rs7589279	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7595396	0.98[ASN][1000 genomes]
rs7601340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7601588	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs7602189	0.81[EUR][1000 genomes]
rs7603105	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7606361	0.82[MEX][hapmap]

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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10169185	CCDC88A	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55648000-55659000	Weak transcription	Adipose Nuclei	Adipose
2	chr2:55650000-55659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:55655200-55659400	Enhancers	Hela-S3	cervix
4	chr2:55655800-55659000	Weak transcription	A549	lung
5	chr2:55657000-55659200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:55657400-55659000	Enhancers	Osteobl	bone
7	chr2:55657800-55659000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:55657800-55659200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:55657800-55659200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:55658000-55659200	Enhancers	NHDF-Ad	bronchial
11	chr2:55658400-55660600	Weak transcription	HepG2	liver
12	chr2:55658800-55659000	Enhancers	Colon Smooth Muscle	Colon
13	chr2:55658800-55659200	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links