Variant report

Variant	rs3856027
Chromosome Location	chr1:70913843-70913844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1145920	0.90[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12023001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182829	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs481654	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs501939	0.90[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs525276	0.90[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs543860	0.81[ASN][1000 genomes]
rs546503	0.92[ASN][1000 genomes]
rs559062	0.90[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs596793	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs608609	0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.80[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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv461828	chr1:70880717-70922360	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv546456	chr1:70880717-70922360	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3856027	HHLA3	cis	lymphoblastoid	seeQTL
rs3856027	DIRAS3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70900200-70914800	Weak transcription	K562	blood
2	chr1:70904600-70915000	Weak transcription	Aorta	Aorta
3	chr1:70907000-70914000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:70908400-70915000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:70908400-70918600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:70908600-70914400	Weak transcription	Liver	Liver
7	chr1:70909000-70928200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:70913000-70916400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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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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