Variant report

Variant	rs974340
Chromosome Location	chr7:25559106-25559107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1502947	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17252583	0.81[ASN][1000 genomes]
rs17266011	0.94[ASN][1000 genomes]
rs17319117	0.94[ASN][1000 genomes]
rs2391135	0.81[ASN][1000 genomes]
rs974339	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
4	esv275528	chr7:25556103-25560512	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs974340	HNRNPA2B1	cis	cerebellum	SCAN
rs974340	NFE2L3	cis	lymphoblastoid	seeQTL
rs974340	KLHL7	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25558000-25559800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:25558600-25560000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr7:25558800-25560200	Enhancers	Primary B cells from peripheral blood	blood
4	chr7:25558800-25560600	Enhancers	Fetal Thymus	thymus
5	chr7:25558800-25562800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr7:25558800-25563000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr7:25559000-25560600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr7:25559000-25562200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr7:25559000-25563200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr7:25559000-25563200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr7:25559000-25563400	Enhancers	Primary T cells from cord blood	blood

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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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