Variant report

Variant	rs6849883
Chromosome Location	chr4:56253682-56253683
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000273257	TF binding region
SRD5A3-AS1	TF binding region
ENSG00000249700	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11133377	0.80[ASN][1000 genomes]
rs11945371	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12641881	0.91[ASN][1000 genomes]
rs13120635	0.87[AMR][1000 genomes]
rs13128180	0.81[AFR][1000 genomes]
rs2048564	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6822746	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663650	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9761521	0.94[AMR][1000 genomes];0.90[EUR][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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6849883	SRD5A3-AS1	cis	Whole Blood	GTEx
rs6849883	TMEM165	cis	Nerve Tibial	GTEx
rs6849883	SRD5A3	cis	Esophagus Mucosa	GTEx
rs6849883	SRD5A3	cis	Whole Blood	GTEx
rs6849883	SRD5A3-AS1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56240400-56259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:56248000-56254000	Weak transcription	Spleen	Spleen
4	chr4:56248000-56259400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:56248200-56261400	Weak transcription	Aorta	Aorta
6	chr4:56249200-56261200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:56251400-56254200	Enhancers	HepG2	liver
8	chr4:56251400-56254400	Flanking Active TSS	K562	blood
9	chr4:56251800-56255000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr4:56252200-56256800	Weak transcription	Fetal Intestine Small	intestine
11	chr4:56252400-56261600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:56252600-56257400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:56252600-56257400	Weak transcription	Brain Substantia Nigra	brain
14	chr4:56253400-56254200	Enhancers	Pancreas	Pancrea

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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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