Variant report

Variant	rs2706916
Chromosome Location	chr7:84001413-84001414
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEMA3D-5	chr7:84001313-84001607	NONHSAT121786

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11973476	0.85[ASN][1000 genomes]
rs1228866	0.96[ASN][1000 genomes]
rs1228868	0.96[ASN][1000 genomes]
rs1228946	0.85[ASN][1000 genomes]
rs1228951	0.93[ASN][1000 genomes]
rs1228956	0.93[ASN][1000 genomes]
rs12667787	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13227369	0.89[ASN][1000 genomes]
rs1520102	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1557791	0.89[ASN][1000 genomes]
rs1634605	0.94[ASN][1000 genomes]
rs16887701	0.84[AFR][1000 genomes]
rs16887703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16887706	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1715518	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17158964	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17158998	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17159006	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1922349	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2106965	0.89[ASN][1000 genomes]
rs2214362	0.84[ASN][1000 genomes]
rs2214749	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2428807	0.93[ASN][1000 genomes]
rs2527522	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527527	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527529	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527530	0.84[ASN][1000 genomes]
rs2527532	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527533	0.84[ASN][1000 genomes]
rs2527535	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527536	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2527537	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527538	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681433	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2681434	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2706903	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2706912	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2706913	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2715032	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2715037	0.83[ASN][1000 genomes]
rs2715044	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2715045	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2715046	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2715047	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2888322	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4016106	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs520178	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526991	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530698	0.96[ASN][1000 genomes]
rs531582	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555632	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs559041	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56144625	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs561955	0.96[ASN][1000 genomes]
rs570638	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs581290	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs625480	0.96[ASN][1000 genomes]
rs641526	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs641950	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs656300	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs667763	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73711542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73711549	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7783073	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2754468	chr7:83851249-84166749	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv888631	chr7:83911271-84010005	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1023848	chr7:83985028-84101774	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2761342	chr7:83985028-84101798	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv534431	chr7:84001059-84138511	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:84001000-84001600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr7:84001000-84002600	Enhancers	NHLF	lung
3	chr7:84001000-84002600	Enhancers	Osteobl	bone
4	chr7:84001200-84001600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:84001200-84001600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:84001200-84001600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr7:84001200-84001600	Flanking Active TSS	NH-A	brain
8	chr7:84001200-84001800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:84001200-84001800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:84001200-84001800	Enhancers	Fetal Heart	heart
11	chr7:84001200-84002600	Enhancers	HSMM	muscle
12	chr7:84001200-84002800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:84001200-84002800	Enhancers	NHDF-Ad	bronchial
14	chr7:84001400-84002000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:84001400-84002000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:84001400-84002200	Enhancers	HMEC	breast
17	chr7:84001400-84002600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:84001400-84003800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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