Variant report

Variant	rs13073658
Chromosome Location	chr3:134565434-134565435
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	chr3:134550436..134552836-chr3:134565260..134567786,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11928990	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489463	0.81[JPT][hapmap]
rs12496060	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072597	0.81[JPT][hapmap];0.93[MEX][hapmap]
rs13079457	0.89[CHB][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs13090529	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1949305	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280156	0.80[AFR][1000 genomes]
rs2292659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2895697	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34894066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35520698	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35600864	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35988574	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60531499	0.83[AFR][1000 genomes]
rs6439529	0.89[CHB][hapmap]
rs6762261	0.89[CHB][hapmap];0.86[MEX][hapmap]
rs6782516	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs6793813	0.81[JPT][hapmap];0.93[MEX][hapmap]
rs6797336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801877	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72984008	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634094	0.83[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][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	nsv877515	chr3:134460368-134591138	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13073658	PPP2R3A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134549800-134569400	Weak transcription	Fetal Brain Male	brain
2	chr3:134563600-134565600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:134564400-134566200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:134564400-134566800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:134564600-134566200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:134564600-134568200	Weak transcription	GM12878-XiMat	blood
7	chr3:134564600-134568600	Weak transcription	Psoas Muscle	Psoas
8	chr3:134564800-134566600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:134564800-134567200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:134565000-134566600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:134565000-134566800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:134565000-134567200	Enhancers	HUVEC	blood vessel
13	chr3:134565200-134565600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr3:134565200-134565600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:134565200-134566600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:134565200-134566600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:134565200-134566800	Enhancers	HepG2	liver
18	chr3:134565200-134566800	Enhancers	HMEC	breast
19	chr3:134565200-134566800	Enhancers	NH-A	brain
20	chr3:134565200-134566800	Enhancers	NHDF-Ad	bronchial
21	chr3:134565400-134565600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:134565400-134565600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:134565400-134565600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:134565400-134565600	Enhancers	Osteobl	bone
25	chr3:134565400-134566000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:134565400-134566200	Enhancers	Fetal Muscle Trunk	muscle
27	chr3:134565400-134566600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:134565400-134566600	Enhancers	Fetal Muscle Leg	muscle
29	chr3:134565400-134566600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:134565400-134566600	Enhancers	Stomach Mucosa	stomach
31	chr3:134565400-134566600	Enhancers	HSMM	muscle
32	chr3:134565400-134566800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:134565400-134566800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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