Variant report

Variant	rs12369709
Chromosome Location	chr12:105639920-105639921
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	chr12:105605767..105607700-chr12:105638996..105640802,2	MCF-7	breast:
2	chr12:105627501..105631320-chr12:105637092..105641109,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1107755	0.98[EUR][1000 genomes]
rs1107757	0.98[EUR][1000 genomes]
rs11112424	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112428	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112434	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1196742	0.83[EUR][1000 genomes]
rs1196745	0.83[EUR][1000 genomes]
rs1196748	0.83[EUR][1000 genomes]
rs1196749	0.83[EUR][1000 genomes]
rs1196753	0.87[EUR][1000 genomes]
rs1196754	0.87[EUR][1000 genomes]
rs1196756	0.83[EUR][1000 genomes]
rs1196764	0.82[EUR][1000 genomes]
rs1196765	0.83[EUR][1000 genomes]
rs1196770	0.89[EUR][1000 genomes]
rs1196772	0.89[EUR][1000 genomes]
rs1196777	0.88[EUR][1000 genomes]
rs1196780	0.91[EUR][1000 genomes]
rs1196782	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196786	0.97[EUR][1000 genomes]
rs1196787	0.96[EUR][1000 genomes]
rs1196789	0.96[EUR][1000 genomes]
rs1196790	0.92[EUR][1000 genomes]
rs1196791	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1196793	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196795	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1196797	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196798	0.81[EUR][1000 genomes]
rs1196800	0.82[EUR][1000 genomes]
rs1196801	0.82[EUR][1000 genomes]
rs1196805	0.82[EUR][1000 genomes]
rs1196806	0.82[EUR][1000 genomes]
rs1196807	0.82[EUR][1000 genomes]
rs1196808	0.81[EUR][1000 genomes]
rs1196811	0.81[EUR][1000 genomes]
rs1196813	0.82[EUR][1000 genomes]
rs1196817	0.82[EUR][1000 genomes]
rs1196819	0.82[EUR][1000 genomes]
rs1196820	0.82[EUR][1000 genomes]
rs1196823	0.82[EUR][1000 genomes]
rs1196825	0.82[EUR][1000 genomes]
rs1196831	0.82[EUR][1000 genomes]
rs1196833	0.82[EUR][1000 genomes]
rs1196839	0.82[EUR][1000 genomes]
rs1196841	0.82[EUR][1000 genomes]
rs1196842	0.82[EUR][1000 genomes]
rs1196844	0.82[EUR][1000 genomes]
rs1196848	0.82[EUR][1000 genomes]
rs1196851	0.82[EUR][1000 genomes]
rs1196853	0.83[EUR][1000 genomes]
rs1196861	0.83[EUR][1000 genomes]
rs1196862	0.82[EUR][1000 genomes]
rs1196864	0.83[EUR][1000 genomes]
rs1196869	0.81[EUR][1000 genomes]
rs1196873	0.81[EUR][1000 genomes]
rs1196874	0.82[EUR][1000 genomes]
rs1206559	0.82[EUR][1000 genomes]
rs1209637	0.96[EUR][1000 genomes]
rs1211276	0.82[EUR][1000 genomes]
rs1211277	0.82[EUR][1000 genomes]
rs1211626	0.97[EUR][1000 genomes]
rs12814458	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12816560	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1444610	0.96[EUR][1000 genomes]
rs1732370	0.82[EUR][1000 genomes]
rs2257156	0.82[EUR][1000 genomes]
rs2440718	0.82[EUR][1000 genomes]
rs2464173	0.82[EUR][1000 genomes]
rs2464175	0.81[EUR][1000 genomes]
rs2464181	0.82[EUR][1000 genomes]
rs2464182	0.81[EUR][1000 genomes]
rs35679386	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67604711	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71441895	0.89[EUR][1000 genomes]
rs73181823	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs873119	0.94[EUR][1000 genomes]
rs935240	0.82[EUR][1000 genomes]
rs935241	0.82[EUR][1000 genomes]
rs935242	0.82[EUR][1000 genomes]
rs935244	0.89[EUR][1000 genomes]
rs935248	0.83[EUR][1000 genomes]
rs935249	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
2	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3429738	chr12:105638759-105642036	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12369709	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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