Variant report

Variant	rs6774875
Chromosome Location	chr3:98699131-98699132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10935513	0.80[ASN][1000 genomes]
rs10935514	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10935587	0.82[ASN][1000 genomes]
rs12632798	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13316760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13319666	0.84[ASN][1000 genomes]
rs1371687	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1383906	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1383907	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1481631	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2062058	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]
rs2062059	0.84[CHB][hapmap]
rs2128052	0.82[ASN][1000 genomes]
rs2340794	0.81[ASN][1000 genomes]
rs2439237	0.89[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2449046	0.86[ASN][1000 genomes]
rs2470853	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470855	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470870	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470872	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]
rs278379	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs278380	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs278381	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs278382	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs278387	0.90[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs278388	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs278390	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs35936923	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4546099	0.89[ASN][1000 genomes]
rs4857416	0.82[ASN][1000 genomes]
rs7615628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7615856	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs828610	0.90[JPT][hapmap]
rs828614	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs828616	0.89[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs828617	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs828621	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs852701	0.90[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs870202	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8833	0.91[GIH][hapmap];0.90[JPT][hapmap]
rs955351	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6774875	DCBLD2	cis	Adipose Subcutaneous	GTEx
rs6774875	ST3GAL6	cis	multi-tissue	Pritchard
rs6774875	DCBLD2	cis	Artery Tibial	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	chr3:98696000-98699600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:98696400-98699800	Enhancers	GM12878-XiMat	blood
4	chr3:98696600-98699800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:98696800-98700400	Enhancers	HUVEC	blood vessel
6	chr3:98697000-98699600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:98697000-98699800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:98697000-98699800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:98697000-98700000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:98697200-98699800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:98697200-98700000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:98697200-98705000	Weak transcription	HSMMtube	muscle
13	chr3:98697400-98699800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:98697600-98699600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:98697600-98699600	Weak transcription	HSMM	muscle
16	chr3:98697600-98700000	Weak transcription	Hela-S3	cervix
17	chr3:98697800-98699600	Weak transcription	HMEC	breast
18	chr3:98697800-98699800	Weak transcription	NHLF	lung
19	chr3:98698000-98700000	Enhancers	NHDF-Ad	bronchial
20	chr3:98698800-98699400	Weak transcription	NH-A	brain
21	chr3:98698800-98699800	Weak transcription	Osteobl	bone
22	chr3:98699000-98699200	Enhancers	NHEK	skin
23	chr3:98699000-98699400	Flanking Active TSS	A549	lung
24	chr3:98699000-98699600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:98699000-98699800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:98699000-98699800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:98699000-98699800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:98699000-98701000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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