Variant report

Variant	rs1571138
Chromosome Location	chr1:46895641-46895642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10489770	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs12029329	0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1535737	0.82[JPT][hapmap]
rs1547180	0.81[ASW][hapmap]
rs2145408	0.93[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2295633	0.81[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs324418	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHD][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs324420	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660346	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4660928	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6429600	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6670926	0.84[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6678149	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6689182	0.81[MEX][hapmap]
rs7555240	0.82[AMR][1000 genomes];0.86[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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1571138	NSUN4	cis	lymphoblastoid	seeQTL
rs1571138	SNORD55	cis	parietal	SCAN
rs1571138	MMACHC	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46872800-46908000	Weak transcription	Right Atrium	heart
2	chr1:46882000-46908200	Weak transcription	Brain Anterior Caudate	brain
3	chr1:46888000-46903600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:46890800-46908200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:46895400-46896600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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