Variant report

Variant	rs1196789
Chromosome Location	chr12:105635276-105635277
allele	A/G
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
ENSG00000136044	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1107755	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1107757	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112348	1.00[CEU][hapmap]
rs11112424	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112428	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112434	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1196742	0.83[EUR][1000 genomes]
rs1196744	0.84[ASN][1000 genomes]
rs1196745	0.83[EUR][1000 genomes]
rs1196748	0.83[EUR][1000 genomes]
rs1196749	0.83[EUR][1000 genomes]
rs1196753	0.88[EUR][1000 genomes]
rs1196754	0.88[EUR][1000 genomes]
rs1196756	0.83[EUR][1000 genomes]
rs1196764	0.83[EUR][1000 genomes]
rs1196765	0.84[EUR][1000 genomes]
rs1196770	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196772	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196777	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1196780	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196782	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196786	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196790	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196791	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196793	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196795	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196797	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196798	0.83[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	0.83[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	0.81[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	0.84[EUR][1000 genomes]
rs1196853	0.83[EUR][1000 genomes]
rs1196859	0.80[EUR][1000 genomes]
rs1196861	0.83[EUR][1000 genomes]
rs1196862	0.82[EUR][1000 genomes]
rs1196864	0.83[EUR][1000 genomes]
rs1196869	0.83[EUR][1000 genomes]
rs1196872	0.84[EUR][1000 genomes]
rs1196873	0.83[EUR][1000 genomes]
rs1196874	0.82[EUR][1000 genomes]
rs1206559	0.82[EUR][1000 genomes]
rs1209637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211276	0.82[EUR][1000 genomes]
rs1211277	0.82[EUR][1000 genomes]
rs1211626	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12369709	0.96[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663565	0.80[EUR][1000 genomes]
rs1732370	0.82[EUR][1000 genomes]
rs2257156	0.84[EUR][1000 genomes]
rs2440718	0.82[EUR][1000 genomes]
rs2464173	0.82[EUR][1000 genomes]
rs2464175	0.83[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	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71441895	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73181823	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs873119	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935240	0.82[EUR][1000 genomes]
rs935241	0.82[EUR][1000 genomes]
rs935242	0.82[EUR][1000 genomes]
rs935244	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs935248	0.83[EUR][1000 genomes]
rs935249	0.84[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	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
rs1196789	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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