Variant report

Variant	rs13215471
Chromosome Location	chr6:49465098-49465099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12175251	0.92[ASN][1000 genomes]
rs13193063	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202158	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17805348	0.84[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs28841337	0.92[ASN][1000 genomes]
rs4562127	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933253	0.84[ASN][1000 genomes]
rs6941331	1.00[YRI][hapmap]
rs9349492	0.92[ASN][1000 genomes]
rs9349493	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369902	0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs9369905	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9381793	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9381794	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9395496	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395501	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9395502	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1019611	chr6:49431569-49470663	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active 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	8 gene(s)	inside rSNPs	diseases
5	esv1793167	chr6:49459978-49466686	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1799212	chr6:49459978-49466791	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13215471	MUT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49432600-49472000	Weak transcription	NHEK	skin
2	chr6:49440400-49465200	Weak transcription	HUVEC	blood vessel
3	chr6:49451400-49467400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:49454000-49465200	Weak transcription	Fetal Brain Male	brain
5	chr6:49458000-49466600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:49458400-49472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:49458600-49473800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:49460400-49473200	Weak transcription	HepG2	liver
9	chr6:49460600-49473600	Weak transcription	Stomach Mucosa	stomach
10	chr6:49461200-49465200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:49461400-49472400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:49461600-49466800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:49461800-49467000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:49462200-49467000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:49465000-49465200	Enhancers	HSMMtube	muscle

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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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