Variant report

Variant	rs2964267
Chromosome Location	chr5:15763516-15763517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11133822	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs11133823	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11748700	0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11958262	0.81[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes]
rs12655356	0.89[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs13170407	0.94[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1505034	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1505037	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867540	0.88[CHB][hapmap]
rs17602392	0.88[CHB][hapmap]
rs17602470	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1875215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1909722	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2937072	1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2964266	0.82[ASN][1000 genomes]
rs2964269	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4133004	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4235556	0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4273603	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4289558	0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs4320259	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4330464	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4395631	0.81[AMR][1000 genomes]
rs4407633	0.88[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs4435862	0.83[CHB][hapmap]
rs4505949	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4582274	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4590179	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4701637	0.89[CHB][hapmap]
rs4702099	0.89[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs4702108	0.81[ASN][1000 genomes]
rs56130171	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6554895	0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs6865314	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6875955	0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs6891925	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6898184	0.93[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7704277	0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7713553	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7713555	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7733271	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs924455	0.89[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	esv2757107	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv2759327	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv2763894	chr5:15714022-15863332	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1031483	chr5:15738485-15926083	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2964267	TRIO	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15758200-15764000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:15762400-15780000	Weak transcription	Fetal Stomach	stomach
3	chr5:15762800-15764200	Enhancers	Fetal Heart	heart

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