Variant report

Variant	rs12040100
Chromosome Location	chr1:155611847-155611848
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10752611	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10908470	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908471	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10908472	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10908479	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264380	0.86[EUR][1000 genomes]
rs11264381	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11264383	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11264386	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11264387	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11264393	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264398	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12022088	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030596	0.89[EUR][1000 genomes]
rs12035524	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12039893	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047626	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12047756	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12093350	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12740629	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12744132	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12746592	0.83[EUR][1000 genomes]
rs12758945	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2048431	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2175391	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2666826	0.85[ASN][1000 genomes]
rs34124416	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34620961	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34632540	0.86[ASN][1000 genomes]
rs348186	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs348196	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3738590	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851912	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3892792	0.92[EUR][1000 genomes]
rs4550031	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475550	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4971095	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427278	0.92[EUR][1000 genomes]
rs6672128	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs678157	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7411786	0.86[EUR][1000 genomes]
rs7521594	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv946419	chr1:155561148-155630744	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12040100	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12040100	GBA	cis	Esophagus Mucosa	GTEx
rs12040100	FDPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155595000-155613000	Weak transcription	Osteobl	bone
2	chr1:155605000-155618000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:155605400-155613000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:155606400-155613000	Weak transcription	HSMM	muscle
5	chr1:155607400-155612000	Weak transcription	HSMMtube	muscle
6	chr1:155607400-155612800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:155607400-155621200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:155607600-155613200	Weak transcription	A549	lung
9	chr1:155608000-155613000	Weak transcription	NH-A	brain
10	chr1:155610400-155614000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:155610600-155614200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:155611200-155613800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
13	chr1:155611800-155613000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:155611800-155613000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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