Variant report

Variant	rs1333065
Chromosome Location	chr1:160759519-160759520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10797086	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127562	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3904492	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs540254	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659569	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695672	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428532	chr1:160671125-160767708	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1333065	SLC25A44	cis	parietal	SCAN
rs1333065	FCRL3	cis	cerebellum	SCAN
rs1333065	ISG20L2	cis	parietal	SCAN
rs1333065	UHMK1	cis	parietal	SCAN
rs1333065	BCAN	cis	parietal	SCAN
rs1333065	PAQR6	cis	parietal	SCAN
rs1333065	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs1333065	NCSTN	cis	cerebellum	SCAN
rs1333065	SNORA42	cis	cerebellum	SCAN
rs1333065	LMNA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160745400-160764800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:160750400-160762000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:160752400-160760400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:160758800-160760600	Flanking Active TSS	GM12878-XiMat	blood
5	chr1:160758800-160762000	Enhancers	Primary B cells from cord blood	blood
6	chr1:160758800-160762000	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:160759000-160759600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:160759000-160760600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:160759200-160759600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
10	chr1:160759200-160760600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:160759200-160760600	Enhancers	Duodenum Mucosa	Duodenum
12	chr1:160759200-160760600	Enhancers	Fetal Thymus	thymus
13	chr1:160759400-160760000	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr1:160759400-160766800	Weak transcription	Spleen	Spleen

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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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