Variant report

Variant	rs1383907
Chromosome Location	chr3:98680953-98680954
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1082403	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1082405	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10935514	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10935587	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636683	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13071075	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13316760	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13319666	0.83[EUR][1000 genomes]
rs1371687	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1383906	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062058	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2128052	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2170404	0.82[ASN][1000 genomes]
rs2340794	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439237	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs2449046	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2470853	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2470855	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2470870	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2470872	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2470873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470877	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470878	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2470880	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278376	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs278379	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs278380	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs278381	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs278382	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs278387	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs278388	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs278390	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap]
rs35483904	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35936923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4546099	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4577404	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4857415	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4857416	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6767370	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6774875	0.90[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6791389	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615628	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7615856	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes]
rs774537	0.88[AMR][1000 genomes]
rs774538	0.80[AMR][1000 genomes]
rs774539	0.83[AMR][1000 genomes]
rs774544	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs774547	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs809575	0.84[AMR][1000 genomes]
rs828605	0.96[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs828610	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs828614	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs828616	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs828617	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs828621	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs852701	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs870202	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8833	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap]
rs955351	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs964163	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9837206	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9880179	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1383907	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx
rs1383907	ST3GAL6	cis	multi-tissue	Pritchard
rs1383907	DCBLD2	cis	Adipose Subcutaneous	GTEx
rs1383907	ZBTB11	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98674400-98681000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:98677200-98681200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:98679400-98681000	Enhancers	NHDF-Ad	bronchial
4	chr3:98679400-98681000	Enhancers	NHLF	lung
5	chr3:98679800-98681000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:98679800-98681400	Flanking Active TSS	A549	lung
7	chr3:98679800-98682400	Flanking Active TSS	NHEK	skin
8	chr3:98680000-98681000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:98680000-98682400	Enhancers	HUVEC	blood vessel
10	chr3:98680400-98681000	Enhancers	HSMM	muscle
11	chr3:98680600-98681400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:98680600-98681600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:98680800-98681000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:98680800-98681000	Enhancers	Fetal Lung	lung
15	chr3:98680800-98681400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:98680800-98681400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:98680800-98681400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr3:98680800-98681400	Flanking Active TSS	HMEC	breast
19	chr3:98680800-98681400	Flanking Active TSS	NH-A	brain
20	chr3:98680800-98681400	Flanking Active TSS	Osteobl	bone
21	chr3:98680800-98681600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:98680800-98681800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:98680800-98682200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:98680800-98682400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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