Variant report

Variant	rs11635790
Chromosome Location	chr15:41880463-41880464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1023193	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079371	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639399	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148316	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739702	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741804	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024626	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025212	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8026760	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8042535	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043421	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11635790	LTK	cis	lung	GTEx
rs11635790	SPTBN5	cis	lung	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41878000-41881000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:41878200-41880600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:41878200-41882600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:41878200-41882600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:41878200-41885600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:41878400-41882600	Weak transcription	HepG2	liver
7	chr15:41878400-41884600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:41878800-41883000	Enhancers	Placenta	Placenta
9	chr15:41878800-41885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:41879200-41881200	Weak transcription	Fetal Intestine Large	intestine
11	chr15:41879200-41881200	Weak transcription	Fetal Intestine Small	intestine
12	chr15:41879400-41880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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