Variant report

Variant	rs11172162
Chromosome Location	chr12:39842812-39842813
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	chr12:39835437..39837020-chr12:39841787..39843770,2	MCF-7	breast:
2	chr12:39835307..39839279-chr12:39842518..39844510,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10877173	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10877201	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11172144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172366	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172616	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172645	0.95[EUR][1000 genomes]
rs11172647	0.95[EUR][1000 genomes]
rs11172687	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11172692	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172697	0.95[EUR][1000 genomes]
rs11172713	0.90[JPT][hapmap]
rs11172722	0.83[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs11172794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11172848	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11172896	0.81[EUR][1000 genomes]
rs11172897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12227286	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12227668	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12228013	1.00[ASW][hapmap];1.00[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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228617	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12229160	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12229370	0.97[EUR][1000 genomes]
rs12230055	0.97[EUR][1000 genomes]
rs1512941	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs17126997	0.81[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17127070	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17127094	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs17127129	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17127138	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271478	1.00[JPT][hapmap]
rs2292491	0.93[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs35790935	0.97[EUR][1000 genomes]
rs35858791	0.97[EUR][1000 genomes]
rs4072006	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4285917	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4294600	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4298947	0.91[EUR][1000 genomes]
rs4378431	0.85[AFR][1000 genomes]
rs4639970	0.97[EUR][1000 genomes]
rs57847223	0.95[EUR][1000 genomes]
rs58036566	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60263267	0.88[AFR][1000 genomes]
rs61258856	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581228	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7133376	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7133599	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7294474	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302302	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7308138	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs73088816	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7309234	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes]
rs73094447	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73094449	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73094488	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7310178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7310871	0.95[EUR][1000 genomes]
rs7312611	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs73268359	0.81[EUR][1000 genomes]
rs74086536	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7966841	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs7970944	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7976275	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7980595	0.93[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11172162	ABCD2	cis	multi-tissue	Pritchard
rs11172162	LRRK2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39838000-39844600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:39838200-39844600	Weak transcription	NHLF	lung
3	chr12:39838200-39845800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:39838600-39843800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:39838600-39843800	Weak transcription	Fetal Brain Female	brain
6	chr12:39839400-39844600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:39839400-39844600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:39839600-39844800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:39842400-39843600	Enhancers	Brain Germinal Matrix	brain
10	chr12:39842600-39843600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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