Variant report

Variant	rs700164
Chromosome Location	chr5:35954588-35954589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10941269	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs700162	0.83[JPT][hapmap]
rs700163	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs700168	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs700173	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs700175	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852235	0.88[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs852236	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1025695	chr5:35902486-36036934	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs700164	IL7R	cis	cerebellum	SCAN
rs700164	C5orf33	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35952000-35957600	Strong transcription	Liver	Liver
2	chr5:35953600-35954800	Strong transcription	Fetal Intestine Small	intestine
3	chr5:35953600-35954800	Enhancers	Fetal Thymus	thymus
4	chr5:35953800-35954600	Enhancers	Thymus	Thymus
5	chr5:35953800-35957800	Strong transcription	Fetal Intestine Large	intestine
6	chr5:35954000-35954800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr5:35954000-35955600	Weak transcription	Psoas Muscle	Psoas
8	chr5:35954200-35954600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:35954200-35954600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:35954200-35954800	Enhancers	Primary T cells from cord blood	blood
11	chr5:35954200-35954800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
12	chr5:35954200-35954800	Enhancers	Dnd41	blood
13	chr5:35954200-35955000	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:35954200-35957400	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:35954400-35954600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:35954400-35954600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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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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