Variant report

Variant	rs2370977
Chromosome Location	chr14:79864472-79864473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12434126	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12434144	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12435532	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12436125	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12879869	0.83[AMR][1000 genomes]
rs12882679	0.84[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes]
rs12884078	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs12896672	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12897000	0.91[CHB][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2167151	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2196442	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2196445	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2197991	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2217888	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2370976	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2370978	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370979	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28889302	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35236866	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35310631	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35441767	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35861800	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36007297	0.81[AMR][1000 genomes]
rs4899743	0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4903850	0.96[CEU][hapmap]
rs4903853	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4903856	0.96[CEU][hapmap];0.84[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61993110	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61993111	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61993112	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61993119	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7150974	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[AMR][1000 genomes];0.94[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	nsv931412	chr14:79420297-79928269	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv902110	chr14:79624492-79998294	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv530072	chr14:79769657-79928269	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv902111	chr14:79807197-79890677	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2370977	ISCA2	cis	cerebellum	SCAN
rs2370977	C14orf169	trans	cerebellum	SCAN
rs2370977	CAMK1G	trans	parietal	SCAN
rs2370977	ANGEL1	cis	cerebellum	SCAN
rs2370977	TMED8	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79856800-79873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:79861600-79872600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:79861800-79874600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr14:79864400-79864600	Enhancers	Brain Germinal Matrix	brain

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