Variant report

Variant	rs6779888
Chromosome Location	chr3:143330927-143330928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11707194	0.88[ASW][hapmap];0.81[GIH][hapmap]
rs11712583	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13089318	0.96[CEU][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1534161	0.94[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1978913	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2030817	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34973048	0.82[AFR][1000 genomes]
rs4425252	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4839645	0.84[AFR][1000 genomes]
rs6773748	0.87[AFR][1000 genomes]
rs6779887	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7632272	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9811274	0.81[ASW][hapmap];0.84[YRI][hapmap]
rs9811842	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6779888	CPB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143297600-143339000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:143300400-143336800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:143318600-143332600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:143322200-143331200	Weak transcription	HMEC	breast
5	chr3:143324200-143340000	Weak transcription	Primary B cells from cord blood	blood
6	chr3:143324400-143353800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:143324600-143331400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:143324600-143331600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:143324600-143336400	Weak transcription	Fetal Stomach	stomach
10	chr3:143328000-143331400	Weak transcription	Adipose Nuclei	Adipose
11	chr3:143328200-143332200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:143328200-143376200	Weak transcription	Ovary	ovary
13	chr3:143328400-143332200	Weak transcription	HSMMtube	muscle
14	chr3:143328400-143346000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:143329600-143331400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:143329600-143337200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:143329800-143331200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:143329800-143334800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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