Variant report

Variant	rs3117600
Chromosome Location	chr4:74731812-74731813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16850137	0.91[JPT][hapmap]
rs2115691	0.87[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap]
rs2367291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097411	0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs3097412	0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap]
rs3111692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3117597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3117598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3117604	0.87[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4074	0.87[JPT][hapmap]
rs516224	0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs58557052	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6858086	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs9991272	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3117600	SEPT11	cis	parietal	SCAN
rs3117600	CKLF	trans	lymphoblastoid	seeQTL
rs3117600	CXCL6	cis	parietal	SCAN
rs3117600	THAP6	cis	parietal	SCAN
rs3117600	G3BP2	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74719400-74733600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:74726000-74734200	Weak transcription	HSMM	muscle
3	chr4:74726200-74733600	Weak transcription	NHDF-Ad	bronchial
4	chr4:74726400-74733800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:74728600-74734200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:74728800-74734000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:74729200-74733600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr4:74730000-74732600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:74730200-74732000	Weak transcription	HMEC	breast
10	chr4:74731200-74732800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:74731400-74734200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr4:74731600-74732200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:74731600-74734000	Enhancers	NHEK	skin
14	chr4:74731600-74734400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:74731800-74732400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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

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