Variant report

Variant	rs1196790
Chromosome Location	chr12:105635368-105635369
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105627699..105634093-chr12:105635156..105638470,6	K562	blood:
2	chr12:105628928..105631591-chr12:105632421..105636831,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1107755	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1107757	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112424	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112428	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112434	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196753	0.82[EUR][1000 genomes]
rs1196754	0.82[EUR][1000 genomes]
rs1196770	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1196772	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1196777	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1196780	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1196782	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196786	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1196787	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196789	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196791	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196793	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196795	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1196797	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1209637	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1211626	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12369709	0.92[EUR][1000 genomes]
rs12814458	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12816560	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1444610	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2272491	0.81[ASN][1000 genomes]
rs2293642	0.85[ASN][1000 genomes]
rs35679386	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794234	0.85[ASN][1000 genomes]
rs3794235	0.85[ASN][1000 genomes]
rs61005937	0.87[ASN][1000 genomes]
rs67604711	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71441895	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73181823	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs873119	0.90[EUR][1000 genomes]
rs935244	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9788027	0.83[ASN][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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1196790	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105630800-105639000	Weak transcription	Pancreas	Pancrea
2	chr12:105630800-105639000	Weak transcription	NHLF	lung
3	chr12:105632400-105638800	Weak transcription	NHDF-Ad	bronchial
4	chr12:105633800-105637000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:105633800-105638800	Weak transcription	Osteobl	bone
6	chr12:105633800-105639000	Weak transcription	Gastric	stomach
7	chr12:105633800-105639200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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