Variant report

Variant	rs10071904
Chromosome Location	chr5:41219940-41219941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10058883	1.00[ASN][1000 genomes]
rs11748237	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12332366	0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12516670	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12516790	0.89[ASN][1000 genomes]
rs12521608	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13436351	0.88[ASN][1000 genomes]
rs1444903	0.97[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4145102	0.83[CHB][hapmap]
rs58840028	0.83[ASN][1000 genomes]
rs59852186	0.89[ASN][1000 genomes]
rs6892389	0.96[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9654390	0.89[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	nsv427717	chr5:41201377-41369202	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv4808	chr5:41203254-41251985	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830269	chr5:41209113-41393536	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10071904	RPL37	cis	parietal	SCAN
rs10071904	PTGER4	cis	cerebellum	SCAN
rs10071904	ZDHHC3	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41218600-41220200	Enhancers	Fetal Intestine Large	intestine
2	chr5:41218600-41220600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:41218800-41220400	Enhancers	Fetal Intestine Small	intestine
4	chr5:41218800-41220600	Enhancers	Brain Anterior Caudate	brain
5	chr5:41219200-41220200	Enhancers	Brain Hippocampus Middle	brain
6	chr5:41219200-41220600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:41219200-41221000	Enhancers	Brain Substantia Nigra	brain
8	chr5:41219400-41220000	Enhancers	Adipose Nuclei	Adipose
9	chr5:41219400-41220000	Enhancers	Brain Angular Gyrus	brain
10	chr5:41219400-41220000	Enhancers	Small Intestine	intestine
11	chr5:41219400-41220200	Enhancers	Fetal Lung	lung
12	chr5:41219400-41220200	Enhancers	Stomach Smooth Muscle	stomach
13	chr5:41219400-41220400	Enhancers	Brain Cingulate Gyrus	brain
14	chr5:41219400-41220600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr5:41219600-41220600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr5:41219600-41221000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr5:41219600-41223600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:41219800-41220400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:41219800-41220800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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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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