Variant report

Variant	rs6478160
Chromosome Location	chr9:118136417-118136418
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10117971	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335141	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2188040	0.81[AFR][1000 genomes]
rs2188041	0.81[AFR][1000 genomes]
rs2269700	1.00[ASW][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs4481680	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478159	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7048282	0.81[AFR][1000 genomes]
rs7469226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7850103	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916553	1.00[ASW][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs9409143	0.82[CEU][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs9409144	0.82[CEU][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs9409145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409146	1.00[CHB][hapmap];1.00[JPT][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]
rs972451	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2761552	chr9:118113846-118157488	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6478160	DNAJC25	cis	parietal	SCAN
rs6478160	SLC31A1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118130600-118142400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:118134400-118138200	Enhancers	HMEC	breast
3	chr9:118134600-118137400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:118134800-118136800	Enhancers	NHDF-Ad	bronchial
5	chr9:118135000-118136600	Enhancers	HepG2	liver
6	chr9:118135200-118136600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:118135200-118136600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:118135200-118136600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr9:118135200-118136600	Enhancers	Stomach Mucosa	stomach
10	chr9:118135200-118136800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:118135200-118136800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:118135600-118137000	Enhancers	NH-A	brain
13	chr9:118135800-118137000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:118135800-118137800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:118135800-118137800	Enhancers	NHEK	skin
16	chr9:118136000-118136800	Flanking Active TSS	A549	lung

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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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