Variant report

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1034762	0.80[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs10783227	0.81[CHB][hapmap]
rs11168337	0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12721428	0.91[JPT][hapmap]
rs1635526	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs1635534	0.88[AMR][1000 genomes]
rs1635535	0.88[AMR][1000 genomes]
rs1635536	0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs1635544	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs1635553	0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1793912	0.88[AMR][1000 genomes]
rs1793913	0.88[AMR][1000 genomes]
rs1793915	0.87[AMR][1000 genomes]
rs1793917	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1793923	0.81[JPT][hapmap]
rs1793931	0.80[CEU][hapmap]
rs1793933	0.85[CEU][hapmap]
rs1793955	0.82[AMR][1000 genomes]
rs1793956	0.84[AMR][1000 genomes]
rs1859444	0.81[CHB][hapmap]
rs1990029	0.85[CEU][hapmap]
rs2070739	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs2276454	0.90[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2276455	0.87[ASN][1000 genomes]
rs2276456	0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2276457	0.86[ASN][1000 genomes]
rs3825404	0.81[CHB][hapmap]
rs3829736	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs917055	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1635550	PRKAG1	cis	parietal	SCAN
rs1635550	SNORA2A	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
4	chr12:48364400-48381200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:48365200-48381600	Weak transcription	Right Atrium	heart
6	chr12:48365400-48381000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:48366200-48381200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:48366200-48381400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48366200-48381600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48372400-48378400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:48374800-48379000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:48375000-48381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:48375200-48381200	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:48376400-48380800	Strong transcription	Fetal Intestine Small	intestine
15	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
16	chr12:48377400-48378800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:48377600-48378400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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