Variant report

Variant	rs2062058
Chromosome Location	chr3:98697349-98697350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr3:98696134-98697661	A549	lung:	n/a	chr3:98697639-98697646 chr3:98697052-98697061
2	FOXA1	chr3:98696933-98697350	HepG2	liver:	n/a	chr3:98697233-98697245
3	EP300	chr3:98696145-98697506	A549	lung:	n/a	chr3:98697459-98697469 chr3:98697256-98697270 chr3:98697299-98697307 chr3:98696636-98696645 chr3:98696637-98696646 chr3:98696403-98696417
4	BCL3	chr3:98696078-98697480	A549	lung:	n/a	chr3:98696636-98696645 chr3:98696637-98696646
5	SP1	chr3:98696112-98697488	A549	lung:	n/a	chr3:98696599-98696608
6	EP300	chr3:98696076-98697519	A549	lung:	n/a	chr3:98697459-98697469 chr3:98697256-98697270 chr3:98697299-98697307 chr3:98696636-98696645 chr3:98696637-98696646 chr3:98696403-98696417
7	FOXA2	chr3:98696900-98697742	A549	lung:	n/a	chr3:98697460-98697472 chr3:98697233-98697245
8	REST	chr3:98696174-98697425	A549	lung:	n/a	n/a
9	GATA3	chr3:98696060-98697575	A549	lung:	n/a	n/a
10	GATA3	chr3:98696844-98697483	A549	lung:	n/a	n/a
11	SP1	chr3:98696040-98697362	HCT-116	colon:	n/a	chr3:98696599-98696608
12	CEBPB	chr3:98696152-98697541	A549	lung:	n/a	chr3:98696405-98696418
13	FOSL2	chr3:98696127-98697459	A549	lung:	n/a	chr3:98697196-98697208 chr3:98696637-98696646 chr3:98696635-98696647 chr3:98696636-98696646 chr3:98696637-98696645 chr3:98696633-98696644 chr3:98696638-98696645

Variant related genes	Relation type
LINC00973	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10935513	0.80[ASN][1000 genomes]
rs10935587	0.82[ASN][1000 genomes]
rs13316760	0.89[ASN][1000 genomes]
rs13319666	0.84[ASN][1000 genomes]
rs1383906	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1383907	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1481631	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2128052	0.82[ASN][1000 genomes]
rs2340794	0.81[ASN][1000 genomes]
rs2439237	0.86[CEU][hapmap]
rs2449046	0.86[ASN][1000 genomes]
rs2470853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470870	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470872	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2470873	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2470877	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2470878	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2470880	0.87[ASN][1000 genomes]
rs35936923	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4546099	0.89[ASN][1000 genomes]
rs4857416	0.82[ASN][1000 genomes]
rs6774875	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615628	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615856	0.81[ASN][1000 genomes]
rs870202	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955351	0.85[ASN][1000 genomes]
rs964163	0.82[ASN][1000 genomes]
rs9837206	0.93[ASN][1000 genomes]
rs9880179	0.85[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2062058	DCBLD2	cis	Artery Tibial	GTEx
rs2062058	DCBLD2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98692000-98699600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:98693600-98697400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:98695000-98697800	Enhancers	HMEC	breast
4	chr3:98695400-98698800	Enhancers	Osteobl	bone
5	chr3:98696000-98699600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:98696200-98697600	Enhancers	Hela-S3	cervix
7	chr3:98696200-98697600	Enhancers	NHEK	skin
8	chr3:98696400-98697400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:98696400-98697600	Enhancers	HSMM	muscle
10	chr3:98696400-98697600	Enhancers	NHDF-Ad	bronchial
11	chr3:98696400-98697800	Enhancers	NHLF	lung
12	chr3:98696400-98698200	Flanking Active TSS	A549	lung
13	chr3:98696400-98699000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:98696400-98699800	Enhancers	GM12878-XiMat	blood
15	chr3:98696600-98697400	Enhancers	HepG2	liver
16	chr3:98696600-98698800	Enhancers	NH-A	brain
17	chr3:98696600-98699800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:98696800-98699000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:98696800-98700400	Enhancers	HUVEC	blood vessel
20	chr3:98697000-98697600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:98697000-98698200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:98697000-98699600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:98697000-98699800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:98697000-98699800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:98697000-98700000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:98697200-98699800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:98697200-98700000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:98697200-98705000	Weak transcription	HSMMtube	muscle

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