Variant report

Variant	rs36125
Chromosome Location	chr3:134694329-134694330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1020434	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17203924	1.00[JPT][hapmap]
rs28211	0.96[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs36064	0.80[TSI][hapmap]
rs36094	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36095	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36096	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36097	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs36099	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36100	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36101	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36102	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36105	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36106	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36108	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36109	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36110	1.00[CEU][hapmap]
rs36111	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36112	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36113	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36114	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs36115	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36116	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36117	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36120	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36121	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36123	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39697	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs39698	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39699	1.00[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs479815	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs574719	1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7644898	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9855772	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][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	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
2	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
3	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
4	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs36125	FAIM	cis	parietal	SCAN
rs36125	EPHB1	cis	multi-tissue	Pritchard
rs36125	STAG1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134671000-134697400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:134677400-134697400	Weak transcription	GM12878-XiMat	blood
3	chr3:134677800-134697000	Weak transcription	Psoas Muscle	Psoas
4	chr3:134678600-134699400	Weak transcription	Aorta	Aorta
5	chr3:134690600-134702400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:134690800-134701200	Weak transcription	Fetal Brain Female	brain
7	chr3:134693200-134697000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:134693200-134697400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:134693200-134701200	Weak transcription	Fetal Brain Male	brain
10	chr3:134693800-134707400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:134694000-134707000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:134694200-134698000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:134694200-134709800	Weak transcription	Brain Germinal Matrix	brain

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