Variant report

Variant	rs542842
Chromosome Location	chr1:70860841-70860842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70860587..70864293-chr1:70864361..70869013,4	K562	blood:
2	chr1:70820167..70822627-chr1:70859878..70861873,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10493473	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10518334	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11209612	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11209613	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12116830	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12118663	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12126226	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12137720	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12725762	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12730494	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12737233	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12741805	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12741941	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12751638	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35481139	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs482291	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs490574	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs508310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs513263	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543860	0.82[EUR][1000 genomes]
rs561926	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618531	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs664051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71500608	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71651454	0.80[AMR][1000 genomes];0.94[EUR][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	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	esv1797324	chr1:70858435-70876569	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	n/a
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs542842	HHLA3	Cis_1M	lymphoblastoid	RTeQTL
rs542842	HHLA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
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