Variant report

Variant	rs7294474
Chromosome Location	chr12:39846127-39846128
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39843581..39846257-chr12:39846498..39848624,2	K562	blood:
2	chr12:39838834..39841587-chr12:39845094..39846761,2	MCF-7	breast:
3	chr12:39845847..39847426-chr12:39847559..39850195,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10877173	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10877201	0.90[JPT][hapmap]
rs11172144	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172162	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172366	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172616	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172645	0.95[EUR][1000 genomes]
rs11172647	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172687	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11172692	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172697	0.95[EUR][1000 genomes]
rs11172713	0.90[JPT][hapmap]
rs11172722	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs11172794	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11172848	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11172896	0.81[EUR][1000 genomes]
rs11172897	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12227286	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12227668	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12228013	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228617	0.90[JPT][hapmap]
rs12229160	0.85[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[JPT][hapmap]
rs17126997	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs17127070	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs17127094	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs17127129	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17127138	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271478	1.00[JPT][hapmap]
rs2292491	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs35790935	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs35858791	0.97[EUR][1000 genomes]
rs4072006	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4285917	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4294600	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs4298947	0.91[EUR][1000 genomes]
rs4378431	0.89[AFR][1000 genomes]
rs4639970	0.97[EUR][1000 genomes]
rs57847223	0.95[EUR][1000 genomes]
rs58036566	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60263267	0.86[AFR][1000 genomes]
rs61258856	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581188	0.82[AFR][1000 genomes]
rs6581228	0.90[JPT][hapmap]
rs7133376	0.90[JPT][hapmap]
rs7133599	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7302302	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7308138	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs73088816	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7309234	0.93[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes]
rs73094447	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73094449	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73094488	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7310178	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7310871	0.95[EUR][1000 genomes]
rs7312611	0.90[JPT][hapmap]
rs73268359	0.81[EUR][1000 genomes]
rs74086536	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7966841	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs7970944	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7976275	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7980595	0.93[CEU][hapmap];1.00[JPT][hapmap]

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	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
2	nsv1044049	chr12:39845078-39922808	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7294474	ABCD2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39843600-39847200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr12:39843800-39847200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:39844600-39846200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:39844600-39847200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr12:39844800-39847000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:39844800-39847200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr12:39845000-39846400	Weak transcription	Fetal Brain Male	brain
8	chr12:39845400-39847000	Enhancers	Brain Germinal Matrix	brain
9	chr12:39845600-39846200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr12:39846000-39846400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:39846000-39846400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr12:39846000-39846600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:39846000-39847000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links