Variant report

Variant	rs4309721
Chromosome Location	chr3:61132698-61132699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001788	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs10049007	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10049287	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10049452	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10049454	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11707984	0.89[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11712122	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12053817	0.89[ASW][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12635622	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13320646	0.89[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13323296	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1371095	0.89[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1473644	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1550343	0.89[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1554601	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1866433	0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1866434	0.89[AFR][1000 genomes]
rs1880213	0.89[AFR][1000 genomes]
rs1916802	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1966136	0.89[ASW][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs1969420	0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2118811	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2886377	0.89[ASW][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4535219	0.81[JPT][hapmap]
rs4688295	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688310	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs56076618	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs61275795	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6445196	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6787511	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807748	0.89[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs753661	0.89[AFR][1000 genomes]
rs7631101	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7631246	0.89[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7636682	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7641177	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs9814044	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9816087	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9819588	0.83[ASW][hapmap];0.87[LWK][hapmap];0.96[YRI][hapmap]
rs9839082	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9844741	0.83[JPT][hapmap]
rs9850125	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9851485	0.89[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9857606	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9861713	0.96[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871451	0.89[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9871598	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv948633	chr3:60993915-61171279	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv834710	chr3:60995631-61148157	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv590425	chr3:61132698-61186550	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4309721	ID2B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61132200-61132800	Enhancers	Fetal Brain Female	brain
2	chr3:61132200-61132800	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr3:61132200-61133200	Enhancers	Fetal Brain Male	brain
4	chr3:61132600-61133000	Enhancers	Brain Germinal Matrix	brain

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