Variant report

Variant	rs1848440
Chromosome Location	chr6:54191970-54191971
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1058768	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1508642	0.82[CEU][hapmap];0.86[MKK][hapmap]
rs1605676	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1813105	0.95[ASN][1000 genomes]
rs1848439	0.88[ASN][1000 genomes]
rs1934791	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7740970	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs9370290	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382323	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474801	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1848440	TINAG	Cis_1M	lymphoblastoid	RTeQTL
rs1848440	GSTA1	cis	parietal	SCAN
rs1848440	IL17A	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54181000-54200400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:54186400-54192400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:54191600-54192000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:54191600-54192200	Strong transcription	Fetal Intestine Large	intestine
5	chr6:54191800-54192400	Weak transcription	Colonic Mucosa	Colon
6	chr6:54191800-54192600	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr6:54191800-54193200	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr6:54191800-54193200	Strong transcription	Rectal Mucosa Donor 29	rectum

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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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