Variant report

Variant	rs529172
Chromosome Location	chr1:78612102-78612103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11162433	0.86[CEU][hapmap]
rs1770307	0.86[CEU][hapmap]
rs586300	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs614836	0.93[CEU][hapmap]
rs6665090	0.86[CEU][hapmap]
rs675799	0.86[CEU][hapmap]
rs681907	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850497	chr1:78596312-78645701	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs529172	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78584200-78630600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:78608800-78614600	Weak transcription	Psoas Muscle	Psoas
3	chr1:78609000-78618000	Weak transcription	Colonic Mucosa	Colon
4	chr1:78609200-78624600	Weak transcription	Pancreas	Pancrea
5	chr1:78609200-78624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:78609400-78612200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:78609400-78619000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:78609600-78620800	Weak transcription	Fetal Intestine Large	intestine
9	chr1:78609800-78613400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:78609800-78614400	Weak transcription	Small Intestine	intestine
11	chr1:78610200-78613600	Weak transcription	HepG2	liver
12	chr1:78610600-78612600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:78610600-78612600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:78611000-78612200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:78611000-78612200	Enhancers	HSMM	muscle
16	chr1:78611000-78612400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:78611000-78612400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:78611000-78612600	Enhancers	Osteobl	bone
19	chr1:78611000-78612800	Enhancers	NHDF-Ad	bronchial
20	chr1:78611000-78613000	Enhancers	Hela-S3	cervix
21	chr1:78611600-78612200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:78611600-78631400	Weak transcription	Liver	Liver

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