Variant report

Variant	rs6702939
Chromosome Location	chr1:78504411-78504412
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000137960	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000074800	Chromatin interaction
ENSG00000230679	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11162404	0.84[YRI][hapmap]
rs11162408	0.94[ASN][1000 genomes]
rs1166698	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs12067638	0.84[ASW][hapmap];0.90[CEU][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12086102	0.84[YRI][hapmap]
rs28735417	0.92[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap]
rs587143	0.82[TSI][hapmap]
rs640935	1.00[YRI][hapmap]
rs6424659	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]
rs6669039	0.84[ASW][hapmap];0.95[CEU][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6699769	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7514180	0.85[ASN][1000 genomes]
rs7537908	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs7539956	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9726525	0.86[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
rs6702939	NEXN	cis	lymphoblastoid	seeQTL
rs6702939	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs6702939	DNAJB4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78486400-78509400	Weak transcription	HSMM	muscle
2	chr1:78499400-78509200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:78499600-78505000	Weak transcription	Pancreas	Pancrea
4	chr1:78499600-78509200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:78500200-78506600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:78503400-78505200	Enhancers	HUVEC	blood vessel
7	chr1:78503800-78504600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:78503800-78505000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:78503800-78505200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:78504000-78506200	Weak transcription	Ovary	ovary
11	chr1:78504000-78510400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:78504200-78509200	Weak transcription	NHLF	lung
13	chr1:78504200-78509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:78504400-78506200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:78504400-78509200	Weak transcription	Hela-S3	cervix
16	chr1:78504400-78510400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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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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