Variant report

Variant	rs6424659
Chromosome Location	chr1:78501215-78501216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11162408	0.94[ASN][1000 genomes]
rs1166698	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs12067638	0.84[ASW][hapmap];0.90[CEU][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28735417	0.92[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs640935	0.86[YRI][hapmap]
rs6669039	0.84[ASW][hapmap];0.95[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6699769	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6702939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514180	0.85[ASN][1000 genomes]
rs7537908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs7539956	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9726525	0.85[CHB][hapmap];0.90[JPT][hapmap]

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	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6424659	DNAJB4	Cis_1M	lymphoblastoid	RTeQTL
rs6424659	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs6424659	NEXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78485000-78504000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:78485400-78504200	Weak transcription	NH-A	brain
3	chr1:78486400-78509400	Weak transcription	HSMM	muscle
4	chr1:78499400-78503600	Weak transcription	Hela-S3	cervix
5	chr1:78499400-78503800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:78499400-78509200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:78499600-78505000	Weak transcription	Pancreas	Pancrea
8	chr1:78499600-78509200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:78500000-78503800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:78500200-78506600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:78500600-78501400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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