Variant report

Variant	rs1196796
Chromosome Location	chr12:105636724-105636725
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10778374	0.81[ASN][1000 genomes]
rs10778375	0.85[ASN][1000 genomes]
rs10861327	0.85[CEU][hapmap]
rs10861328	0.85[CEU][hapmap]
rs10861329	0.86[CEU][hapmap]
rs10861330	0.86[CEU][hapmap]
rs10861335	0.86[CEU][hapmap]
rs10861336	0.86[CEU][hapmap]
rs1109432	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112347	0.85[CEU][hapmap]
rs11112350	0.86[CEU][hapmap]
rs11112351	0.86[CEU][hapmap]
rs11112414	0.90[JPT][hapmap]
rs11112436	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11612252	0.86[CEU][hapmap]
rs11613261	0.86[CEU][hapmap]
rs1196750	0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196758	0.96[CEU][hapmap]
rs1196766	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196767	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196776	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196778	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196779	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196785	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196804	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs1196809	0.84[EUR][1000 genomes]
rs1196812	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs1196814	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs1196816	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs1196822	0.83[EUR][1000 genomes]
rs1196835	0.83[EUR][1000 genomes]
rs1196836	0.93[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs1196838	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1196840	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1196854	0.86[EUR][1000 genomes]
rs1196856	0.86[EUR][1000 genomes]
rs1196860	0.83[EUR][1000 genomes]
rs1196865	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs1196866	0.86[EUR][1000 genomes]
rs1196867	0.85[EUR][1000 genomes]
rs1196868	0.86[EUR][1000 genomes]
rs1196878	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196882	0.89[CEU][hapmap]
rs1201657	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1201658	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs12581638	0.85[CEU][hapmap]
rs1317941	0.87[ASN][1000 genomes]
rs17036869	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs1732378	0.89[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs1732379	0.86[EUR][1000 genomes]
rs1732384	0.86[JPT][hapmap]
rs2246510	0.96[CEU][hapmap]
rs2264066	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs2374448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440708	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440713	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2440717	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs2440719	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs4144468	0.86[CEU][hapmap]
rs4964127	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4964346	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6539196	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539197	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs727888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308195	0.85[CEU][hapmap]
rs7309320	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969800	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9143	0.89[CHB][hapmap];0.86[JPT][hapmap]

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
rs1196796	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 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
8	chr12:105636400-105637200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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