Variant report

Variant	rs28211
Chromosome Location	chr3:134730661-134730662
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1020434	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs194179	0.93[ASN][1000 genomes]
rs253881	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs253882	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs36064	0.80[MEX][hapmap];0.81[TSI][hapmap]
rs36073	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs36094	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36095	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36096	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36097	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs36099	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36100	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36101	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36102	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36105	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36106	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36108	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36109	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36110	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs36111	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36112	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36113	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36114	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36115	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36116	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36117	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36120	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36121	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36123	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36125	0.96[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs39697	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs39698	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs39699	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40435	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs479815	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574719	0.89[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7644898	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9855772	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv877517	chr3:134709951-134805581	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv829731	chr3:134711713-134885064	Strong transcription Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28211	COPB2	cis	cerebellum	SCAN
rs28211	EPHB1	cis	multi-tissue	Pritchard
rs28211	STAG1	cis	parietal	SCAN
rs28211	FAIM	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134728000-134742000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:134729000-134735200	Weak transcription	Fetal Brain Female	brain

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