Variant report

Variant	rs12123144
Chromosome Location	chr1:76550209-76550210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10443175	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162083	0.82[JPT][hapmap]
rs12123760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251467	0.82[JPT][hapmap]
rs1251470	0.93[ASN][1000 genomes]
rs1251471	0.93[ASN][1000 genomes]
rs1251473	0.93[ASN][1000 genomes]
rs1251474	0.93[ASN][1000 genomes]
rs1251484	0.91[CEU][hapmap]
rs1251485	0.91[CEU][hapmap]
rs1251492	0.81[EUR][1000 genomes]
rs1251496	0.81[EUR][1000 genomes]
rs1251504	0.81[EUR][1000 genomes]
rs1251505	0.81[EUR][1000 genomes]
rs1251511	0.81[EUR][1000 genomes]
rs1266117	0.81[EUR][1000 genomes]
rs1763465	1.00[JPT][hapmap]
rs17659615	0.82[EUR][1000 genomes]
rs34354538	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12123144	ABHD14A	trans	brain	seeQTL
rs12123144	RASL11B	trans	brain	seeQTL
rs12123144	PRRT1	trans	brain	seeQTL
rs12123144	PPP2R5D	trans	brain	seeQTL
rs12123144	ST6GALNAC3	cis	Thyroid	GTEx
rs12123144	MTFR1	trans	brain	seeQTL
rs12123144	ACP6	trans	brain	seeQTL
rs12123144	CASQ1	trans	brain	seeQTL
rs12123144	FAM82B	trans	brain	seeQTL
rs12123144	STMN2	trans	brain	seeQTL
rs12123144	ATP1A1	trans	brain	seeQTL
rs12123144	MYPOP	trans	brain	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76541200-76551200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:76542200-76553200	Weak transcription	Fetal Intestine Large	intestine
3	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:76545400-76551400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:76545600-76552200	Weak transcription	Fetal Intestine Small	intestine
6	chr1:76545600-76558200	Weak transcription	Left Ventricle	heart
7	chr1:76545800-76550600	Enhancers	Fetal Lung	lung
8	chr1:76546200-76550600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:76547400-76552200	Weak transcription	Fetal Kidney	kidney
10	chr1:76548000-76561800	Weak transcription	Fetal Brain Female	brain
11	chr1:76548400-76576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:76548800-76550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:76549000-76550400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:76549000-76552400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:76549000-76556200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:76549000-76556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:76549200-76550400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:76549200-76550400	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:76549200-76551000	Weak transcription	Stomach Mucosa	stomach
20	chr1:76549200-76552800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:76549200-76556600	Weak transcription	Brain Anterior Caudate	brain
22	chr1:76549200-76556800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:76549400-76550600	Enhancers	Brain Hippocampus Middle	brain
24	chr1:76549400-76550800	Enhancers	Brain Substantia Nigra	brain
25	chr1:76549800-76550600	Enhancers	Brain Angular Gyrus	brain
26	chr1:76549800-76551200	Enhancers	Pancreas	Pancrea
27	chr1:76550000-76550400	Enhancers	Fetal Stomach	stomach
28	chr1:76550000-76550800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr1:76550000-76551200	Enhancers	H9 Cell Line	embryonic stem cell
30	chr1:76550000-76556600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:76550200-76550600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr1:76550200-76551000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:76550200-76556800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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