Variant report

Variant	rs11165173
Chromosome Location	chr1:95046746-95046747
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10874864	0.99[ASN][1000 genomes]
rs10874865	0.99[ASN][1000 genomes]
rs11165169	0.96[ASN][1000 genomes]
rs11165174	0.99[ASN][1000 genomes]
rs11165176	0.98[ASN][1000 genomes]
rs12028955	0.99[ASN][1000 genomes]
rs12354010	0.99[ASN][1000 genomes]
rs12402343	0.99[ASN][1000 genomes]
rs12406950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12742434	0.96[ASN][1000 genomes]
rs34182043	0.98[ASN][1000 genomes]
rs841685	0.90[JPT][hapmap]
rs841687	0.90[JPT][hapmap]
rs841688	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871279	chr1:95028981-95083836	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11165173	GFI1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95044200-95047000	Enhancers	NHEK	skin
2	chr1:95044200-95048400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:95044400-95047000	Enhancers	NHLF	lung
4	chr1:95044400-95048200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:95044400-95048400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:95044400-95048400	Enhancers	HMEC	breast
7	chr1:95044600-95046800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:95044600-95047000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:95044600-95047400	Enhancers	HSMMtube	muscle
10	chr1:95046000-95065400	Weak transcription	Fetal Intestine Large	intestine
11	chr1:95046400-95047000	Weak transcription	Aorta	Aorta
12	chr1:95046400-95047000	Enhancers	NH-A	brain
13	chr1:95046400-95047200	Weak transcription	Placenta	Placenta
14	chr1:95046400-95047400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:95046400-95048800	Enhancers	Hela-S3	cervix
16	chr1:95046400-95055200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:95046600-95047000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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